Search

Abstract Background Mammals rely on the circadian clock network to regulate daily systemic metabolism and physiological activities. The liver is an important peripheral organ in mammals, and it has a unique circadian rhythm regulation process. As the only mammals that can fly, bats have attracted much research attention due to their nocturnal habits and life histories. However, few research reports exist concerning the circadian rhythms of bat liver gene expression and the relevant biological clock regulation mechanisms in the liver. Results In this study, the expression levels of liver genes of Asian particolored bats were comparatively analyzed using RNA-seq at four different time points across 24 h. A total of 996 genes were found to be rhythmic, accounting for 65% of the total number of expressed genes. The critical circadian rhythm genes Bmal1, Rev-erbα, Cry, and Ror in the liver exhibited different expression patterns throughout the day, and participated in physiological processes with rhythmic changes, including Th17 cell differentiation (ko04659), antigen processing and presentation (ko04612), the estrogen signaling pathway (ko04915), and insulin resistance (ko04931). In addition, previous studies have found that the peroxisome proliferator-activated receptor (PPAR) metabolic signaling pathway (ko03320) may play a vital role in the rhythmic regulation of the metabolic network. Conclusions This study is the first to demonstrate diurnal changes in bat liver gene expression and related physiological processes. The results have thus further enriched our understanding of bats’ biological clocks.

Abstract Background Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes. Results Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle. By examining large-scale genome-wide association studies for 46 human traits (average n = 327,973) and 45 cattle traits (average n = 24,635), we reveal that the heritability of complex traits in both species is significantly more enriched in transcriptionally conserved than diverged genes across tissues. Conclusions In summary, our study provides a comprehensive comparison of transcriptomes between humans and cattle, which might help decipher the genetic and evolutionary basis of complex traits in both species.

IntroductionFat-tail in sheep is considered as an important energy reservoir to provide energy as a survival buffer during harsh challenges. However, fat-tail is losing its importance in modern sheep industry systems and thin-tailed breeds are more desirable. Using comparative transcriptome analysis to compare fat-tail tissue between fat- and thin-tailed sheep breeds provides a valuable approach to study the complex genetic factors associated with fat-tail development. However, transcriptomic studies often suffer from issues with reproducibility, which can be improved by integrating multiple studies based on a meta-analysis.MethodsHence, for the first time, an RNA-Seq meta-analysis on sheep fat-tail transcriptomes was performed using six publicly available datasets.Results and discussionA total of 500 genes (221 up-regulated, 279 down-regulated) were identified as differentially expressed genes (DEGs). A jackknife sensitivity analysis confirmed the robustness of the DEGs. Moreover, QTL and functional enrichment analysis reinforced the importance of the DEGs in the underlying molecular mechanisms of fat deposition. Protein-protein interactions (PPIs) network analysis revealed the functional interactions among the DEGs and the subsequent sub-network analysis led to identify six functional sub-networks. According to the results of the network analysis, down-regulated DEGs in green and pink sub-networks (like collagen subunits IV, V, and VI, integrins 1 and 2, SCD, SCD5, ELOVL6, ACLY, SLC27A2, and LPIN1) may impair lipolysis or fatty acid oxidation and cause fat accumulation in tail. On the other hand, up-regulated DEGs, especially those are presented in green and pink sub-networks (like IL6, RBP4, LEPR, PAI-1, EPHX1, HSD11B1, and FMO2), might contribute to a network controlling fat accumulation in the tail of sheep breed through mediating adipogenesis and fatty acid biosynthesis. Our results highlighted a set of known and novel genes/pathways associated with fat-tail development, which could improve the understanding of molecular mechanisms behind fat deposition in sheep fat-tail.

Ramie (Boehmeria nivea L.), belonging to Urticaceae, is principally used for fabric production. It is a well-known natural fiber material for ancient clothing. Despite its important position and application value, the understanding on genetic regulation mechanism of fiber quality is limited. Here, we generate a chromosome-scale, high-quality reference genome of ramie, in which, approximately 90.2% of the assembled sequences have been anchored to 14 pseudochromosomes. Totally 27,664 protein-coding genes are predicted which cover 268.24 Mb region of the genome. Comparative genomic analysis reveals that 2,047 and 796 gene clusters expand and contract, respectively, underlying significant genes in plant hormone signal transduction and cellulose/lignin biosynthesis pathways. An integrative analysis combining quantitative trait loci (QTL), comparative transcriptomic data, and cytological experiments unravels the molecular regulatory mechanism of ramie fiber fineness, especially the critical regulating role of ethylene. This study would lay a solid foundation for the research of molecular biology in ramie and provide valuable reference for the improvement of high-quality fiber varieties.

Ciliates usually with big cell sizes, complex morphological structures, and diverse life cycles, are good model organisms for studying cell proliferation regulation of eukaryotes. Up to date, the molecular regulation mechanisms for the vegetative cell cycle and encystment of these ciliates are poorly understood. Here, transcriptomes of Apodileptus cf. visscheri, which has an asexual vegetative cell cycle and is apt to encyst when environmental conditions become unfavorable, were sequenced to enrich our related knowledge. In this study, three replicates were sequenced for each of four cell stages, including initial period of growth, morphogenesis, cell division, and resting cyst. The significant transcription differences, involving cell cycle, biosynthesis, and energy metabolism pathways, were revealed between the resting cyst and vegetative cell cycle. Further investigations showed that the cell cycle pathway was enriched during morphogenesis stage and cell division stage. Compared to the initial period of growth stage, the differentially expressed genes involved in cellular components and molecular function were significantly enriched during cell division stage, while cellular components and biological processes were significantly enriched during morphogenesis stage. These provide novel insights into a comprehensive understanding at the molecular level of the survival and adaptive mechanism of unicellular eukaryotes. [ABSTRACT FROM AUTHOR]

Bupleurum chinense DC. is a well-known traditional Chinese medicinal plant that produces saikosaponins (SSs), which possess hepatoprotective, antipyretic, and anti-inflammatory activities. Methyl jasmonate (MeJA) is a signalling phytohormone that can increase the accumulation of SSs in the root of Bupleurum plants. However, the molecular understanding of MeJA-mediated SS biosynthesis is not clear. Therefore, it is necessary to explore the molecular mechanism underlying the response of B. chinense DC. to MeJA in roots. In this study, we performed comparative transcriptome analysis of B. chinense DC. roots with different MeJA treatment times. In total, 104,057 unigenes were identified, of which 4053 were differentially expressed genes (DEGs). Most of the DEGs were downregulated after MeJA treatment, and GO enrichment analysis showed that they were mainly related to biological processes involved in stress responses and development. A total of 88 DEGs encoding enzymes known to be involved in the SS synthesis pathway were found, and most were significantly downregulated within 24 h. Based on the DEGs, 99 transcription factors (TFs) belonging to the AP2/ERF, WRKY, bZIP, ZFP, and bHLH families with different expression patterns were also identified. Further integrated analysis indicated that 20 DEGs involved in the SS synthesis pathway and 12 DEGs encoding TFs presented strong correlations with the SS contents, and these DEGs may be critical for the biosynthesis and regulation of SSs. These findings will be critical for further study of the response of B. chinense DC. to MeJA for SS biosynthesis. [ABSTRACT FROM AUTHOR]

Bacterial canker of tomato is a systemic disease caused by Clavibacter michiganensis (Cm), which poses a grave threat to tomato production worldwide. Towards the identification of genes underlying resistance to Cm infection, the transcriptome of the resistant inbred backcross line IBL2353 carrying the Rcm2.0 locus derived from Solanum habrochaites LA407 and the susceptible Solanum lycopersicum line Ohio88119 was comparatively analyzed after Cm inoculation, and the analysis focused on the genes with different expression patterns between resistant and susceptible lines. Gene ontology (GO) analysis revealed that top terms of differentially expressed genes comprised ubiquitin protein ligases, transcription factors, and receptor kinases. Then we screened out some genes which are potentially associated with the defense response against Cm infection in IBL2353 including the wall-associated receptor kinase-like 20 (WAKL20), and virus-induced gene silencing showed it contributes resistance to Cm infection. In addition to Cm-induced genes related to resistance, the expression of eight homologs from six susceptibility (S) gene families was analyzed. These putative resistance and susceptibility genes are valuable resources for molecular resistance breeding and contribute to the development of new control methods in tomato. [ABSTRACT FROM AUTHOR]

Abies beshanzuensis, an extremely rare and critically endangered plant with only three wild adult trees globally, is strongly mycorrhizal-dependent, leading to difficulties in protection and artificial breeding without symbiosis. Root hair morphogenesis plays an important role in the survival of mycorrhizal symbionts. Due to the lack of an effective genome and transcriptome of A. beshanzuensis, the molecular signals involved in the root hair development remain unknown, which hinders its endangered mechanism analysis and protection. Herein, transcriptomes of radicles with root hair (RH1) and without root hair (RH0) from A. beshanzuensis in vitro plantlets were primarily established. Functional annotation and differentially expressed gene (DEG) analysis showed that the two phenotypes have highly differentially expressed gene clusters. Transcriptome divergence identified hormone and sugar signaling primarily involved in root hair morphogenesis of A. beshanzuensis. Weighted correlation network analysis (WGCNA) coupled with quantitative real-time PCR (qRT-PCR) found that two hormone–sucrose–root hair modules were linked by IAA17, and SUS was positioned in the center of the regulation network, co-expressed with SRK2E in hormone transduction and key genes related to root hair morphogenesis. Our results contribute to better understanding of the molecular mechanisms of root hair development and offer new insights into deciphering the survival mechanism of A. beshanzuensis and other endangered species, utilizing root hair as a compensatory strategy instead of poor mycorrhizal growth. [ABSTRACT FROM AUTHOR]

Abstract Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains.

Abstract Background Sheath blight is an important disease caused by Rhizoctonia cerealis that affects wheat yields worldwide. No wheat varieties have been identified with high resistance or immunity to sheath blight. Understanding the sheath blight resistance mechanism is essential for controlling this disease. In this study, we investigated the response of wheat to Rhizoctonia cerealis infection by analyzing the cytological changes and transcriptomes of common wheat 7182 with moderate sensitivity to sheath blight and H83 with moderate resistance. Results The cytological observation showed that the growth of Rhizoctonia cerealis on the surface and its expansion inside the leaf sheath tissue were more rapid in the susceptible material. According to the transcriptome sequencing results, a total of 88685 genes were identified in both materials, including 20156 differentially expressed genes (DEGs) of which 12087 was upregulated genes and 8069 was downregulated genes. At 36 h post-inoculation, compared with the uninfected control, 11498 DEGs were identified in resistant materials, with 5064 downregulated genes and 6434 upregulated genes, and 13058 genes were detected in susceptible materials, with 6759 downregulated genes and 6299 upregulated genes. At 72 h post-inoculation, compared with the uninfected control, 6578 DEGs were detected in resistant materials, with 2991 downregulated genes and 3587 upregulated genes, and 7324 genes were detected in susceptible materials, with 4119 downregulated genes and 3205 upregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included biosynthesis of secondary metabolites, carbon metabolism, plant hormone signal transduction, and plant–pathogen interaction. In particular, phenylpropane biosynthesis pathway is specifically activated in resistant variety H83 after infection. Many DEGs also belonged to the MYB, AP2, NAC, and WRKY transcription factor families. Conclusions Thus, we suggest that the normal functioning of plant signaling pathways and differences in the expression of key genes and transcription factors in some important metabolic pathways may be important for defending wheat against sheath blight. These findings may facilitate further exploration of the sheath blight resistance mechanism in wheat and the cloning of related genes.

Procambarus clarkii (Girard, 1852) has important economic value in China and internationally. In this research, the comparative transcriptome analysis was used to reveal molecular mechanisms of influences of photoperiod and light intensity on ovarian development in P. clarkii for the first time. Some genes (such as laminin , collagen , integrin beta , catenin) and pathways (including TGF-beta signaling pathway, focal adhesion, ECM–receptor interaction) associated with ovarian development and oocyte maturation were significantly upregulated. Some genes related to circadian clock (such as CLK , PER) were identified in this research. The results indicated that when light intensity or photoperiod increased, P. clarkii could up-regulate the expression levels of the laminin and collagen , thereby synthesizing related proteins, promoting meiosis of the oocytes, thus increasing the number of oocytes in the ovary. At the same time, P. clarkii could up-regulate the expression levels of integrin beta , integrin alpha 6 , and diacylglycerol to synthesize related proteins, thereby promoting the formation of proteins and fats such as triglycerides, these proteins and fats can provide material basis for maturation and development of oocytes, resulting in oocyte maturation and ovarian development. P. clarkii could synthesize related proteins by upregulating expression levels of genes (such as catenin), these proteins or hormones can adhere to other actins (such as integrins), thereby stabilizing the morphology of the oocytes and ensuring normal development. Meantime, the increase in light intensity or photoperiod could cause release GSH and VTG, resulting in oocytes development and maturation. The data in this research can reveal molecular mechanisms of impacts of photoperiod and light intensity on oocyte maturation and ovarian development in P. clarkii , can offer crucial genomic data for studying developmental mechanisms of ovary and oocyte in crustacean. [Display omitted] • Effects of light intensity and photoperiod on ovarian development of P. clarkii were studied from multiple levels. • Some DEGs and signaling pathways were discovered for the first time in ovaries of P. clarkii. • Increasing in light conditions promoted ovarian development of P. clarkii. [ABSTRACT FROM AUTHOR]

Terpenoids, as the main components of the floral scent, exhibit interspecific variations and spatial specificity in Chrysanthemum genus. Here, we selected two primary species as the ancestors of C. morifolium along with two classic cultivars to investigate the influence of domestication on the variations in emission and production of floral terpenoids. The results indicated that the wild relatives emitted and accumulated higher levels of terpenoids in their disc florets and phyllaries & receptacles compared to the cultivars. Six gene modules associated with terpenoid production in three floral organs were characterized through WGCNA. Furthermore, 28 terpene synthase (TPS) genes were identified from both wild relatives and cultivars by comparative transcriptome database. In vitro enzymatic activity assay revealed that several products of monoterpenoids (α -pinene and α -terpinene) and sesquiterpenoids (β -farnesene, α -copaene and γ -curcumene), were commonly catalyzed by TPSs identified from wild relatives and cultivars. Nevertheless, we found that β -myrcene, β -elemene, β -cadinene and β -caryophyllene were predominantly produced by TPSs in the wild relatives, while d -limonene and β -copaene were specifically catalyzed by TPSs in the cultivars. It was also observed that the expression of the CiLSTPS3 gene could be associated with the emission and accumulation of β -caryophyllene in floral scent. Overall, the complex biochemical functions of TPSs, along with their varying expression patterns, significantly contribute to the interspecific variations of floral terpenoids in the Chrysanthemum genus. Our findings provide new insights into the molecular and biochemical mechanisms underlying the impact of domestication on the production of floral terpenoids in Chrysanthemum. • Higher content and emission of terpenoids were detected in the disc florets and phyllaries & receptacles of wild relatives. • 28 terpene synthase genes were functionally identified in wild relatives and cultivars. • The spatial expression pattern of CiLSTPS3 showed a positive correlation with the content and emission of β -caryophyllene. • The complex activities of TPSs and varied expression of TPSs led to the interspecific variation of terpenoid production. [ABSTRACT FROM AUTHOR]

Abstract Background Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually to the aquaculture industry of L. crocea. Although there have been some studies on the pathogenesis for cryptocaryonosis, little is known about the innate defense mechanism of different immune organs of large yellow croaker. Results In order to analyze the roles of long non-coding RNAs and genes specifically expressed between immune organs during the infection of C. irritans, in this study, by comparing transcriptome data from different tissues of L. crocea, we identified tissue-specific transcripts in the gills and skin, including 507 DE lncRNAs and 1592 DEGs identified in the gills, and 110 DE lncRNAs and 1160 DEGs identified in the skin. Furthermore, we constructed transcriptome co-expression profiles of L. crocea gill and skin, including 7,503 long noncoding RNAs (lncRNAs) and 23,172 protein-coding genes. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DEGs and the target genes of the DE lncRNAs in the gill were specifically enriched in several pathways related to immune such as HIF-1 signaling pathway. The target genes of DE lncRNAs and DEGs in the skin are specifically enriched in the complement and coagulation cascade pathways. Protein–protein interaction (PPI) network analysis identified 3 hub genes including NFKBIA, TNFAIP3 and CEBPB, and 5 important DE lncRNAs including MSTRG.24134.4, MSTRG.3038.5, MSTRG.27019.3, MSTRG.26559.1, and MSTRG.10983.1. The expression patterns of 6 randomly selected differentially expressed immune-related genes were validated using the quantitative real-time PCR method. Conclusions In short, our study is helpful to explore the potential interplay between lncRNAs and protein coding genes in different tissues of L. crocea post C. irritans and the molecular mechanism of pathogenesis for cryptocaryonosis. Highlights Skin and gills are important sources of pro-inflammatory molecules, and their gene expression patterns are tissue-specific after C. irritans infection. 15 DEGs and 5 DE lncRNAs were identified as hub regulatory elements after C. irritans infection The HIF-1 signaling pathway and the complement and coagulation cascade pathway may be key tissue-specific regulatory pathways in gills and skin, respectively.

Pareuchiloglanis macrotrema is a glyptosternoid fish belonging to the Siluriform family and is endemic to the Qinghai-Tibet Plateau tributaries. P. macrotrema is an ideal model for studying the adaptive evolution of fish at high altitudes. P. macrotrema has two attaching livers connected to the main liver, a common feature in most Sisoridae fishes but is a special phenomenon relative to other vertebrates. Using RNA-Seq, 42 differentially expressed genes were found between the main liver and attaching liver, of which 31 were upregulated and 11 were downregulated in the main liver. The major differentially expressed genes between the main liver and attaching liver of P. macrotrema are related to metabolism, immunity, and digestive processes. Meanwhile, a comparative transcriptome analysis was carried out on P. macrotrema fish and six non-plateau Siluriformes fishes. We found 268 positively selected genes in P. macrotrema that are related to energy metabolism, immunity, and hypoxic responses. The findings of this study highlight the gene expression differences between the main liver and attaching livers of Sisoridae fishes and provide greater insight into the evolution of Tibetan fishes. [ABSTRACT FROM AUTHOR]

BACKGROUND: Acetylcholine (ACh), as a classical neurotransmitter, plays great roles in the nervous system. There is increasing evidence of its non‐neuronal roles in regulating basic cell functions in vertebrates. However, knowledge about the non‐neuronal cholinergic system in insects is scarce. RESULTS: A comparative transcriptome analysis was performed to investigate differences in the key molecular components of the cholinergic system between the head and ovary. The results showed that expression levels of most cholinergic system‐related genes were higher in the head than in the ovary, and some cholinergic components were absent in the ovary. ACh contents ranged from 0.1 to 1.3 μg mg−1 of wet weight during the development of the ovary, and weak acetylcholinesterase activity was also detected. Moreover, the ovary has a capacity for ACh synthesis. Bromoacetylcarnitine (BrACar), a specific carnitine acetyltransferase (CarAT) inhibitor, greatly inhibits ACh synthesis by 83.83% in ovary homogenates, but bromoacetylcholine (BrACh), a specific choline acetyltransferase (ChAT) inhibitor, has no effect on ACh synthesis in the ovary. These findings indicate that non‐neuronal ACh in the ovary is only catalyzed by CarAT. CONCLUSION: This study reveals the existence of the non‐neuronal cholinergic system in the ovary of M. separata, whose synthesis and release mechanisms are different from those of the head. These results provide novel insights into the non‐neuronal cholinergic system in insects, and will be valuable in the discovery of new target genes and the future development of green pest control. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

As a consequence of long-term coevolution and natural selection, the leaves of mulberry (Morus alba) trees have become the best food source for silkworms (Bombyx mori). Nevertheless, the molecular and genomic basis of defense response remains largely unexplored. In the present study, we assessed changes in the transcriptome changes of mulberry in response to silkworm larval feeding at 0, 3, and 6 h. A total of 4709 (up = 2971, down = 1738) and 3009 (up = 1868, down = 1141) unigenes were identified after 3 and 6 h of silkworm infestation, respectively. MapMan enrichment analysis results show structural traits such as leaf surface wax, cell wall thickness and lignification form the first physical barrier to feeding by the silkworms. Cluster analysis revealed six unique temporal patterns of transcriptome changes. We predicted that mulberry promoted rapid changes in signaling and other regulatory processes to deal with mechanical damage, photosynthesis impairment, and other injury caused by herbivores within 3–6 h. LRR-RK coding genes (THE1, FER) was predicted participated in perception of cell wall perturbation in mulberry responding to silkworm feeding. Ca2+ signal sensors (CMLs), ROS (OST1, SOS3), RBOHD/F, CDPKs, and ABA were part of the regulatory network after silkworm feeding. Jasmonic acid (JA) signal transduction was predicted to act in silkworm feeding response, 10 JA signaling genes (such as OPR3, JAR1, and JAZ1) and 21 JA synthesis genes (such as LOX2, AOS, and ACX1) were upregulated after silkworm feeding for 3 h. Besides, genes of "alpha-Linolenic acid metabolism" and "phenylpropanoid biosynthesis" were activated in 3 h to reprogram secondary metabolism. Collectively, these findings provided valuable insights into silkworm herbivory-induced regulatory and metabolic processes in mulberry, which might help improve the coevolution of silkworm and mulberry. [ABSTRACT FROM AUTHOR]

Bifenazate is a novel acaricide that has been widely used to control spider mites. Interestingly, we found bifenazate had a biological activity against the diamondback moth (Plutella xylostella), one of the most economically important pests on crucifer crops around the world. However, the molecular mechanisms underlying the response of P. xylostella to bifenazate treatment are not clear. In this study, we first estimated the LC30 dose of bifenazate for third-instar P. xylostella larvae. Then, in order to identify genes that respond to the treatment of this insecticide, the comparative transcriptome profiles were used to analyze the gene expression changes in P. xylostella larvae after exposure to LC30 of bifenazate. In total, 757 differentially expressed genes (DEGs) between bifenazate-treated and control P. xylostella larvae were identified, in which 526 and 231 genes were up-regulated and down-regulated, respectively. The further Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the xenobiotics metabolisms pathway was significantly enriched, with ten detoxifying enzyme genes (four P450s, five glutathione S-transferases (GSTs), and one UDP-Glucuronosyltransferase (UGT)) were up-regulated, and their expression patterns were validated by qRT-PCR as well. Interestingly, the present results showed that 17 cuticular protein (CP) genes were also remarkably up-regulated, including 15 CPR family genes. Additionally, the oxidative phosphorylation pathway was found to be activated with eight mitochondrial genes up-regulated in bifenazate-treated larvae. In contrast, we found some genes that were involved in tyrosine metabolism and purine pathways were down-regulated, indicating these two pathways of bifenazate-exposed larvae were significantly inhibited. In conclusion, the present study would help us to better understand the molecular mechanisms of sublethal doses of bifenazate detoxification and action in P. xylostella. [ABSTRACT FROM AUTHOR]

Aeromonas hydrophila infections are common in aquaculture. Our previous studies found that the A. hydrophila B11 strain can survive in fish macrophages for at least 24 h and the two‐component system EnvZ/OmpR may be involved in intracellular survival. To reveal the role and mechanism of the two‐component system EnvZ/OmpR in intracellular survival of A. hydrophila, the genes of envZ/ompR were silenced by shRNAi. The results showed that the survival rates of the envZ‐RNAi and ompR‐RNAi strains were only 2.05% and 3.75%, respectively, which were decreased by 91% and 83.6% compared with that of the wild‐type strain. The escape ability of envZ‐RNAi and ompR‐RNAi was also decreased by 51.4% and 19.7%, respectively. The comparative transcriptome analysis revealed that the functional genes directly related to bacterial intracellular survival mainly included the genes related to anti‐stress capacity, and the genes related to Zn2+ and Mg2+ transport. Further research confirmed that two‐component system EnvZ/OmpR can regulate the expression of the important molecular chaperones, such as groEL, htpG, dnaK, clpB and grpE. The expression of these molecular chaperones in wild‐type strain was up‐regulated with the increase in H2O2 concentrations, while the expression of these molecular chaperones in silent strains did not change significantly. Cells that phagocytosed wild‐type strain had higher ROS content than cells that phagocytosed silent strains. Two‐component system EnvZ/OmpR could also regulate zinc transporter (znuA, znuB, znuC) and zinc efflux protein (zntA) to maintain zinc homeostasis in cells, thus affecting the ability of bacteria to survive in phagocytes. Moreover, two‐component system EnvZ/OmpR could affect the growth and intracellular survival of A. hydrophila by regulating the expression of MgtA, MgtC and MgtE and participating in bacterial Mg2+ homeostasis in fish macrophages. [ABSTRACT FROM AUTHOR]

Forsythia suspensa (Thunb.) has been widely used in traditional medicines in Asia. According to the 2020 edition of Chinese Pharmacopoeia, phillyrin is the main active ingredient in F. suspensa, which is effective in clearing heat, reducing swelling, and dispersing nodules. F. suspensa leaf is a non-toxic substance and it can be used to make a health tea. Here, we combine elicitors and transcriptomics to investigate the inducible biosynthesis of the phillyrin from the F. suspensa. After the fruits and leaves of F. suspensa were treated with different concentrations of methyl jasmonate (MeJA), the content of phillyrin in the fruits reached a peak at 200 µM MeJA for 12 h, but which was decreased in leaves. To analyze the differences in key enzyme genes involved in the phillyrin biosynthesis, we sequenced the transcriptome of F. suspensa leaves and fruits treated with 200 µM MeJA for 12 h. We hypothesized that nine genes related to coniferin synthesis including: F. suspensa UDP-glycosyltransferase (FsUGT); F. suspensa 4-coumarate coenzyme CoA ligase (Fs4CL); and F. suspensa Caffeoyl-CoA O-methyltransferase (FsCCoAOMT) etc. The qRT-PCR analysis of genes related to phillyrin biosynthesis was consistent with RNA-seq analysis. We also investigated the dynamic changes of genes in F. suspensa leaves and fruits at different time points after 200 µM MeJA treatment, which laid the foundation for further study of the molecular mechanisms regulating the biosynthesis of phillyrin. [ABSTRACT FROM AUTHOR]

Molting is one of the most important biological processes of crustacean species, and a number of molecular mechanisms facilitate this complex procedure. However, the understanding of the immune mechanisms underlying crustacean molting cycle remains very limited. This study performed transcriptome sequencing in hemolymph and hepatopancreas of the swimming crab (Portunus trituberculatus) during the four molting stages: post-molt (AB), inter-molt (C), pre-molt (D), and ecdysis (E). The results showed that there were 78,572 unigenes that were obtained in the hemolymph and hepatopancreas of P. trituberculatus. Further analysis showed that 98 DEGs were involved in immunity response of hemolymph and hepatopancreas, and most of the DEGs participated in the process of signal transduction, pattern recognition proteins/receptors, and antioxidative enzymes system. Specifically, the key genes and pathway involved in signal transduction including the GPCR126, beta-integrin, integrin, three genes in mitogen-activated protein kinase (MAPK) signaling cascade (MAPKKK10, MAPKK4, and p38 MAPK), and four genes in Toll pathway (Toll-like receptor, cactus, pelle-like kinase, and NFIL3). For the pattern recognition proteins/receptors, the lowest expression level of 11 genes was found in the E stage, including C-type lectin receptor, Ctype lectin domain family 6 member A and SRB3/C in the hemolymph, and hepatopancreatic lectin 4, C-type lectin, SRB, Down syndrome cell adhesion molecule homolog, Down syndrome cell adhesion molecule isoform, and A2M. Moreover, the expression level of copper/zinc superoxide dismutase isoform 4, glutathione peroxidase, glutathione S-transferase, peroxiredoxin, peroxiredoxin 6, and dual oxidase 2 in stage C or stage D significantly higher than that of stage E or stage AB. These results fill in the gap of the continuous transcriptional changes that are evident during the molting cycle of crab and further provided valuable information for elucidating the molecular mechanisms of immune regulation during the molting cycle of crab. [ABSTRACT FROM AUTHOR]

The widespread and endemic circulation of porcine reproductive and respiratory syndrome virus (PRRSV) cause persistent financial losses to the swine industry worldwide. In 2017, NADC34-like PRRSV-2 emerged in northeastern China and spread rapidly. The dynamics analysis of immune perturbations associated with novel PRRSV lineage is still incomplete. This study performed a time-course transcriptome sequencing of NADC34-like PRRSV strain YC-2020-infected porcine alveolar macrophages (PAMs) and compared them with JXA1-infected PAMs. The results illustrated dramatic changes in the host's differentially expressed genes (DEGs) presented at different timepoints after PRRSV infection, and the expression profile of YC-2020 group is distinct from that of JXA1 group. Functional enrichment analysis showed that the expression of many inflammatory cytokines was up-regulated following YC-2020 infection but at a significantly lower magnitude than JXA1 group, in line with the trends for most interferon-stimulated genes (ISGs) and their regulators. Meanwhile, numerous components of histocompatibility complex (MHC) class II and phagosome presented a stronger transcription suppression after the YC-2020 infection. All results imply that YC-2020 may induce milder inflammatory responses, weaker antiviral processes, and more severe disturbance of antigen processing and presentation compared with HP-PRRSV. Additionally, LAPTM4A, GLMP, and LITAF, which were selected from weighted gene co-expression network analysis (WGCNA), could significantly inhibit PRRSV proliferation. This study provides fundamental data for understanding the biological characteristics of NADC34-like PRRSV and new insights into PRRSV evolution and prevention. [ABSTRACT FROM AUTHOR]

The evolution of C4 photosynthesis involved multiple anatomical and physiological modifications, yet our knowledge of the genetic regulation involved remains elusive. In this study, systematic analyses were conducted comparing the C3–C4 intermediate Moricandia suffruticosa and its C3 relative Brassica napus (rapeseed). We found that the leaves of M. suffruticosa had significantly higher vein density than those of B. napus , and the vein density was further increased in M. suffruticosa under drought and heat stress. Moreover, the bundle sheath distance, as the mean distance from the outer wall of one bundle sheath to the outer wall of an adjacent one, decreased and the number of centripetal chloroplasts in bundle sheath cells was found to be altered in M. suffruticosa leaves under drought and heat treatments. These results suggest that abiotic stress can induce a change in an intermediate C3–C4 anatomy towards a C4-like anatomy in land plants. By integrating drought and heat factors, co-expression network and comparative transcriptome analyses between M. suffruticosa and B. napus revealed that inducible auxin signaling regulated vascular development, and autophagy-related vesicle trafficking processes were associated with this stress-induced anatomical change. Overexpressing three candidate genes, MsERF02 , MsSCL01 , and MsDOF01 , increased leaf vein density and/or enhanced photosynthetic assimilation and drought adaptability in the transgenic lines. The findings of this study may improve our understanding of the genetic regulation and evolution of C4 anatomy. [ABSTRACT FROM AUTHOR]

Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish can be attractive models to study senescence because of their unique aging characteristics. The lifespan of fish varies widely, and several species can live for over 200 years. Moreover, some fish show anti-aging features and indeterminate growth throughout their life. Therefore, exploring the aging mechanism in fish could provide new insights into vertebrate aging. To this end, we conducted RNA sequencing (RNA-seq) assays for various organs and growth stages of zebrafish and compared the data with previously published RNA-seq data of rats. Age-associated differentially expressed genes (DEGs) for all zebrafish tissue samples reveal the upregulation of circadian genes and downregulation of hmgb3a. On one hand, a comparative analysis of DEG profiles associated with aging between zebrafish and rats identifies upregulation of circadian genes and downregulation of collagen genes as conserved transcriptome changes. On the other hand, in zebrafish, upregulation of autophagy-related genes in muscles and AP-1 transcription factor genes in various tissues is observed, which may imply fish-specific anti-aging characteristics. Consistent with our knowledge of mammalian aging, DEG profiles related to tissue senescence are observed in rats. We also detect age-associated downregulation of muscle homeostasis and differentiation-related genes in zebrafish gills, indicating a fish-specific senescence phenotype. Our results indicate both common and different aging profiles between fish and mammals, which could be used for future translational research. [ABSTRACT FROM AUTHOR]

Leaf stalk-stem angle is an important agronomic trait influencing melon architecture, photosynthetic efficiency, and crop yield. However, the mechanisms governing leaf stalk-stem angle, particularly in melon, are not well understood. In this study, we explored the comparative transcriptome in the expanded architecture line Y164 and the compact plant architecture line Z151 at 30 days after pollination. Phytohormones were measured at the leaf stalk-angle site at the same time in these two lines using liquid chromatography (LC) tandem mass spectrometry (MS) (LC-MS/MS). The phytohormones and transcriptomes were jointly analyzed. Differential hormone profiling revealed that the levels of 1-aminocyclopropane-1-carboxylate (ACC) and 12-oxophytodienoic acid (OPDA) in the large-angled line Y164 were significantly higher than those in the small-angled line Z151. These differences were quantified as 2.1- and 2.8-fold increases, respectively. Conversely, the content of isopentenyl adenosine (IPA) was significantly elevated in Z151, with a 3.8-fold higher concentration relative to Y164. Transcriptome analysis identified a total of 1709 differently expressed genes (DEGs), with a predominant enrichment in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to photosynthesis and plant hormone signal transduction. Similarly, photosynthesis and the hormone metabolic process were predominantly enriched in the biological process of Gene Ontology (GO) terms. Further integration of transcriptome and hormone analyses substantiated the close relationship between melon leaf stalk-stem angle and phytohormones, especially ACC, OPDA and IPA. Selected DEGs from phytohormone signal transduction were validated. Detailed analysis of DEGs highlighted the potential role of genes such as GH3s ( LOC103490488 , LOC103490483 ), SUARs ( LOC107991561 , LOC103497281 and LOC103489067 ), ARFs ( LOC103503893 , LOC103493078 ) and five genes in abscisic acid pathway. In summary, our findings strongly suggest a direct correlation between phytohormones and the leaf stalk-stem angles in melon., Competing Interests: The authors declare there are no competing interests., (©2024 Mao et al.)

Abstract Background Paphiopedilum hirsutissimum is a member of Orchidaceae family that is famous for its ornamental value around the globe, it is vulnerable due to over-exploitation and was listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents its trade across borders. Variation in flower color that gives rise to different flower patterns is a major trait contributing to its high ornamental value. However, the molecular mechanism underlying color formation in P. hirsutissimum still remains unexplored. In the present study, we exploited natural variation in petal and labellum color of Paphiopedilum plants and used comparative transcriptome analysis as well as pigment measurements to explore the important genes, metabolites and regulatory pathways linked to flower color variation in P. hirsutissimum. Result We observed that reduced anthocyanin and flavonoid contents along with slightly higher carotenoids are responsible for albino flower phenotype. Comparative transcriptome analysis identified 3287 differentially expressed genes (DEGs) among normal and albino labellum, and 3634 DEGs between normal and albino petals. Two genes encoding for flavanone 3-hydroxylase (F3H) and one gene encoding for chalcone synthase (CHS) were strongly downregulated in albino labellum and petals compared to normal flowers. As both F3H and CHS catalyze essentially important steps in anthocyanin biosynthesis pathway, downregulation of these genes is probably leading to albino flower phenotype via down-accumulation of anthocyanins. However, we observed the downregulation of major carotenoid biosynthesis genes including VDE, NCED and ABA2 which was inconsistent with the increased carotenoid accumulation in albino flowers, suggesting that carotenoid accumulation was probably controlled at post-transcriptional or translational level. In addition, we identified several key transcription factors (MYB73, MYB61, bHLH14, bHLH106, MADS-SOC1, AP2/ERF1, ERF26 and ERF87) that may regulate structural genes involved in flower color formation in P. hirsutissimum. Importantly, over-expression of some of these candidate TFs increased anthocyanin accumulation in tobacco leaves which provided important evidence for the role of these TFs in flower color formation probably via regulating key structural genes of the anthocyanin pathway. Conclusion The genes identified here could be potential targets for breeding P. hirsutissimum with different flower color patterns by manipulating the anthocyanin and carotenoid biosynthesis pathways.

Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.

Eriocheir sinensis is widely appreciated by the surrounding population due to its culinary delicacy and rich nutrients. The E. sinensis breeding industry is very prosperous and molting is one of the important growth characteristics. Research on the regulation of molting in E. sinensis is still in the initial stages. There is currently no relevant information on the regulatory mechanisms of heart development following molting. Comparative transcriptome analysis was used to study developmental regulation mechanisms in the heart of E. sinensis at the post-molt and inter-molt stages. The results indicated that many regulatory pathways and genes involved in regeneration, anti-oxidation, anti-aging and the immune response were significantly upregulated after molting in E. sinensis. Aside from cardiac development, the differentially expressed genes (DEGs) were relevant to myocardial movement and neuronal signal transduction. DEGs were also related to the regulation of glutathione homeostasis and biological rhythms in regard to anti-oxidation and anti-aging, and to the regulation of immune cell development and the immune response. This study provides a theoretical framework for understanding the regulation of molting in E. sinensis and in other economically important crustaceans. [ABSTRACT FROM AUTHOR]

Simple Summary: The size of antlers varies among species; antlers of the wapiti (Cervus canadensis xanthopygus) grow much faster than those of its close relative the sika deer (Cervus nippon hortulorum) in the same growing period. This contrast provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, the reference transcriptomes of the antler reserve mesenchyme (RM) tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared, and interactive relationships and expression patterns of hub genes were identified and analysed. We identified that RNA Binding Motif Protein X-Linked (RBMX) gene was under strongly positive selection. One gene found to interact with RBMX was methyltransferase-like 3 (METTL3), an oncogene that could promote translation of cancer cell proteins. There was a contrasting relationship in expression level between RBMX and METTL3 genes in the RM tissue. We believe our study can provide a better understanding of rapid antler growth at the molecular level in particular and endochondral ossification in general. The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcriptomes of antler RM tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared. The results showed that: a total of 44,485 reference full-length transcripts of antlers were obtained; 254 highly expressed transcripts (HETs) and 1936 differentially expressed genes (DEGs) were enriched and correlated principally with translation, endochondral ossification and ribosome; 228 genes were found to be under strong positive selection and would thus be important for the evolution of wapiti and sika deer; among the alternative splicing variants, 381 genes were annotated; and 4 genes with node degree values greater than 50 were identified through interaction network analysis. We identified a negative and a positive regulator for rapid antler growth, namely RNA Binding Motif Protein X-Linked (RBMX) and methyltransferase-like 3 (METTL3), respectively. Overall, we took advantage of this significant difference in growth rate and performed the comparative analyses of the antlers to identify key specific factors that might be candidates for the positive or negative regulation of phenomenal antler growth rate. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technology has been widely used and continuously optimized. As one kind of high-throughput sequencing technology, RNA sequencing (RNA-seq) can effectively detect complete transcriptome information, which brings prospects for plant researches. Conifers are a family of Coniferopsida, mainly including Cupressaceae, Taxodiaceae, Pinaceae and Taxaceae trees. Presently, the whole genome sequencing (WGS) of many crops and broadleaf trees have been completed, while that of conifer species are limited due to huge data volume and complicated repeat sequences. Therefore, RNA-seq is one of the most important and practical methods for exploring conifers genes. This review introduced the analysis processes of RNA-seq, and highlighted the applications and prospects of RNA-seq in conifers molecular genetics, which might provide references for future genetic improvement and molecular breeding in conifer species. Key message: The review presented RNA-seq applications in conifers, including comparative transcriptome, exploring functional genes, developing molecular markers, and detecting miRNAs. Moreover, the future perspectives were discussed. [ABSTRACT FROM AUTHOR]

Fusarium oxysporum is a main causative agent of tobacco root rot, severely affecting tobacco growth. Here, 200 F. oxysporum strains were isolated and examined for their virulence toward tobacco plants. These strains were divided into disease class 1-3 (weak virulence), 4-6 (moderate virulence), and 7-9 (strong virulence). To understand the virulence mechanism of F. oxysporum, a comparative transcriptome study was performed using weak, moderate, and strong virulence-inducing strains. The results showed that expression levels of 1,678 tobacco genes were positively correlated with virulence levels, while expression levels of 3,558 genes were negatively associated with virulence levels. Interestingly, the expression levels of ATP synthase genes were positively correlated with F. oxysporum virulence. To verify whether ATP synthase gene expression is associated with F. oxysporum virulence, 5 strains each of strong, moderate, and weak virulence-inducing strains were tested using qRT-PCR. The results confirmed that ATP synthase gene expression is positively correlated with virulence levels. Knock-out mutants of ATP synthase genes resulted in a relatively weak virulence compared to wild-type as well as the inhibition of F. oxysporum-mediated suppression of NtSUC4, NtSTP12, NtHEX6, and NtSWEET, suggesting that ATP synthase activity is also associated with the virulence. Taken together, our analyses show that ATP synthases are key genes for the regulation of F. oxysporum virulence and provide important information for understanding the virulence mechanism of F. oxysporum in tobacco root rot. [ABSTRACT FROM AUTHOR]

Background: Mammals rely on the circadian clock network to regulate daily systemic metabolism and physiological activities. The liver is an important peripheral organ in mammals, and it has a unique circadian rhythm regulation process. As the only mammals that can fly, bats have attracted much research attention due to their nocturnal habits and life histories. However, few research reports exist concerning the circadian rhythms of bat liver gene expression and the relevant biological clock regulation mechanisms in the liver. Results: In this study, the expression levels of liver genes of Asian particolored bats were comparatively analyzed using RNA-seq at four different time points across 24 h. A total of 996 genes were found to be rhythmic, accounting for 65% of the total number of expressed genes. The critical circadian rhythm genes Bmal1, Rev-erbα, Cry, and Ror in the liver exhibited different expression patterns throughout the day, and participated in physiological processes with rhythmic changes, including Th17 cell differentiation (ko04659), antigen processing and presentation (ko04612), the estrogen signaling pathway (ko04915), and insulin resistance (ko04931). In addition, previous studies have found that the peroxisome proliferator-activated receptor (PPAR) metabolic signaling pathway (ko03320) may play a vital role in the rhythmic regulation of the metabolic network. Conclusions: This study is the first to demonstrate diurnal changes in bat liver gene expression and related physiological processes. The results have thus further enriched our understanding of bats' biological clocks. [ABSTRACT FROM AUTHOR]

Ganoderma lucidum is an edible mushroom highly regarded in the traditional Chinese medicine. To better understand the molecular mechanisms underlying fruiting body development in G. lucidum, transcriptome analysis based on RNA sequencing was carried out on different developmental stages: mycelium (G1); primordium (G2); young fruiting body (G3); mature fruiting body (G4); fruiting body in post-sporulation stage (G5). In total, 26,137 unigenes with an average length of 1078 bp were de novo assembled. Functional annotation of transcriptomes matched 72.49% of the unigenes to known proteins available in at least one database. Differentially expressed genes (DEGs) were identified between the evaluated stages: 3135 DEGs in G1 versus G2; 120 in G2 versus G3; 3919 in G3 versus G4; and 1012 in G4 versus G5. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs identified in G1 versus G2 revealed that, in addition to global and overview maps, enriched pathways were related to amino acid metabolism and carbohydrate metabolism. In contrast, DEGs identified in G2 versus G3 were mainly assigned to the category of metabolism of amino acids and their derivatives, comprising mostly upregulated unigenes. In addition, highly expressed unigenes associated with the transition between different developmental stages were identified, including those encoding hydrophobins, cytochrome P450s, extracellular proteases, and several transcription factors. Meanwhile, highly expressed unigenes related to meiosis such as DMC1, MSH4, HOP1, and Mek1 were also analyzed. Our study provides important insights into the molecular mechanisms underlying fruiting body development and sporulation in G. lucidum. [ABSTRACT FROM AUTHOR]

Floret opening and closure are critical for rice to complete reproductive development. To further understand the molecular mechanism of floret opening and closure in rice, RNA-seq was performed on the floret of Indica and Japonica rice in the state of 1-h before floret opening, at the opening and closure, respectively. Our results show that many differentially expressed genes are produced throughout the floret opening and closure of both Indica and Japonica rice. Differentially expressed genes shared between Indica and Japonica rice at floret opening were involved in seven metabolic pathways, including plant hormone signal transduction, MAPK signaling pathway-plant, starch and sucrose metabolism, alpha-Linolenic acid metabolism, plant–pathogen interaction, diterpenoid biosynthesis, glucuronate interconversions, phenylpropanoid biosynthesis, compared to 1 h before floret opening. In addition, the expression patterns of some genes, OsJAZ13, OsJAZ11 and OsCML1 which the above metabolic pathways, were different between Indica and Japonica rice. Compared to the floret opening, the differentially expressed genes at floret closure were mainly involved in the following three metabolic pathways: Circadian rhythm-plant, sesquiterpenoid and triterpenoid biosynthesis, starch and sucrose metabolism, and thiamine metabolism. This study provides insights into revealing the molecular mechanism of floret opening and closure in rice. [ABSTRACT FROM AUTHOR]

Salt stress seriously reduced the yield and quality of watermelon and restricted the sustainable development of the watermelon industry. However, the molecular mechanism of watermelon in response to salt stress is still unclear. In this study, 150 mmol·L−1 NaCl was used to deal with the seedlings of salt-tolerant and salt-sensitive watermelon varieties. Physiological characteristics showed that salt stress significantly reduced the biomass of watermelon seedlings and the accumulation of K+ in roots and leaves and significantly increased the content of Na+, Cl−, and malondialdehyde (MDA). Compared with the salt-sensitive variety, the salt-tolerant variety had higher K+ accumulation, lower Cl−, Cl− accumulation, and MDA content in roots and leaves. Then, RNA-seq was performed on roots and leaves in normal culture and under 150 mmol·L−1 NaCl treatment. A total of 21,069 genes were identified by RNA-seq analysis, of which 1412 were genes encoding transcription factors (TFs). In the comparison groups of roots and leaves, 122 and 123 shared differentially expressed genes (DEGs) were obtained, respectively. Gene ontology (GO) annotation and KEGG enrichment results showed that there were many identical GO terms and KEGG pathways in roots and leaves, especially the pathways that related to sugar or energy (ATP or NADP+/NADPH). In addition, some DEGs related to salt tolerance were identified, such as plant hormone indole-3-acetic acid (IAA) and gibberellin (GA) signal transduction pathway-related genes, K+/Na+/Ca2+-related genes, lignin biosynthesis-related genes, etc. At the same time, we also identified some TFs related to salt tolerance, such as AP2-EREBP, bZIP, bHLH, MYB, NAC, OFP, TCP, and WRKY and found that these TFs had high correlation coefficients with salt tolerance-related genes, indicating that they might have a potential regulatory relationship. Interestingly, one TCP TF (Cla97C09G174040) co-exists both in roots and leaves, and it is speculated that it may be regulated by miR319 to improve the salt tolerance of watermelon. [ABSTRACT FROM AUTHOR]

M. incognita is a major parasitic plant disease in watermelon production, causing serious economic losses. Although there are many studies on root-knot nematode, the resistance mechanism is still unclear. In this study, in order to fully understand the mechanism of watermelon resistance to root-knot nematode, the relatively strongly resistant 'Hongzi watermelon' variety and the susceptible 'M16' watermelon variety were used as materials, combined with RNA sequencing (RNA-seq), to analyze the expression abundance of resistant and susceptible varieties at 0, 2, 8 and 15 days post-infection (DPI) by M. incognita. The number of differentially expressed genes (DEGs) in the four comparison groups (A0_B0, A1_B1, A2_B2 and A3_B3) was 3645, 2306, 4449 and 2362, respectively, and there were 835 shared DEGs among them. GO annotation and KEGG pathway enrichment analysis showed that 835 DEGs were mainly involved in phenylpropane biosynthesis and carbon metabolism. Furthermore, lignin-biosynthesis-related genes (4CL (4-coumaric acid-CoA ligase), C3H (coumaric acid 3-hydroxylase), CSE (caffeoyl shikimate esterase), COMT (caffeic acid-O-methyltransferase), CCR (cinnamyl CoA reductase) and PRX (peroxidase)), defense-related proteins (UDP-glucoronosyl/UDP-glucosyl transferase, UGT84A13; salicylic acid binding protein, SABP2) and some transcription factors (TFs) were highlighted, which may be potential candidate genes for further analysis in the infection process of M. incognita. These results suggest that watermelon can achieve resistance to M. incognita by increasing the content of lignin and phenols in root or improving ROS level. These RNA-seq data provide new knowledge for future functional studies and will be helpful to further elucidate the molecular mechanism of resistance to M. incognita in watermelon. [ABSTRACT FROM AUTHOR]

Culm color variation is an interesting phenomenon that contributes to the breeding of new varieties of ornamental plants during domestication. De-domesticated variation is considered ideal for identifying and interpreting the molecular mechanisms of plant mutations. However, the variation in culm color of bamboo remains unknown. In the present study, yellow and green culms generated from the same rhizome of Phyllostachys vivax cv. Aureocaulis (P. vivax) were used to elucidate the molecular mechanism of culm color formation. Phenotypic and physiological data showed that environmental suitability was higher in green culms than in yellow culms. High-throughput sequencing analysis showed 295 differentially expressed genes (DEGs) and 22 differentially expressed miRNAs (DEMs) in two different colored bamboo culms. There were 103 DEM-DEG interaction pairs, of which a representative “miRNA-mRNA” regulatory module involved in photosynthesis and pigment metabolism was formed by 14 DEM-DEG pairs. The interaction of the three key pairs was validated by qPCR and dual-luciferase assays. This study provides new insights into the molecular mechanism of miRNAs involved in P. vivax culm color formation, which provides evidence for plant de-domestication and is helpful for revealing the evolutionary mechanism of bamboo.

Abstract Background Blueberry (Vaccinium spp.) is characterized by the production of berries that are smaller than most common fruits, and the underlying mechanisms of fruit size in blueberry remain elusive. V. corymbosum ‘O’Neal’ and ‘Bluerain’ are commercial southern highbush blueberry cultivars with large- and small-size fruits, respectively, which mature ‘O’Neal’ fruits are 1 ~ 2-fold heavier than those of ‘Bluerain’. In this study, the ontogenetical patterns of ‘O’Neal’ and ‘Bluerain’ hypanthia and fruits were compared, and comparative transcriptomic analysis was performed during early fruit development. Results V. corymbosum ‘O’Neal’ and ‘Bluerain’ hypanthia and fruits exhibited intricate temporal and spatial cell proliferation and expansion patterns. Cell division before anthesis and cell expansion after fertilization were the major restricting factors, and outer mesocarp was the key tissue affecting fruit size variation among blueberry genotypes. Comparative transcriptomic and annotation analysis of differentially expressed genes revealed that the plant hormone signal transduction pathway was enriched, and that jasmonate-related TIFYs genes might be the key components orchestrating other phytohormones and influencing fruit size during early blueberry fruit development. Conclusions These results provided detailed ontogenetic evidence for determining blueberry fruit size, and revealed the important roles of phytohormone signal transductions involving in early fruit development. The TIFY genes could be useful as markers for large-size fruit selection in the current breeding programs of blueberry.

Abstract Background Polyploid plants often exhibit enhanced stress tolerance. The underlying physiological and molecular bases of such mechanisms remain elusive. Here, we characterized the drought tolerance of autotetraploid sour jujube at phenotypic, physiological and molecular levels. Results The study findings showed that the autotetraploid sour jujube exhibited a superior drought tolerance and enhanced regrowth potential after dehydration in comparison with the diploid counterpart. Under drought stress, more differentially expressed genes (DEGs) were detected in autotetraploid sour jujube and the physiological responses gradually triggered important functions. Through GO enrichment analysis, many DEGs between the diploid and autotetraploid sour jujube after drought-stress exposure were annotated to the oxidation–reduction process, photosystem, DNA binding transcription factor activity and oxidoreductase activity. Six reactive oxygen species scavenging-related genes were specifically differentially expressed and the larger positive fold-changes of the DEGs involved in glutathione metabolism were detected in autotetraploid. Consistently, the lower O2− level and malonaldehyde (MDA) content and higher antioxidant enzymes activity were detected in the autotetraploid under drought-stress conditions. In addition, DEGs in the autotetraploid after stress exposure were significantly enriched in anthocyanin biosynthesis, DNA replication, photosynthesis and plant hormone, including auxin, abscisic acid and gibberellin signal-transduction pathways. Under osmotic stress conditions, genes associated with the synthesis and transport of osmotic regulators including anthocyanin biosynthesis genes were differentially expressed, and the soluble sugar, soluble protein and proline contents were significantly higher in the autotetraploid. The higher chlorophyll content and DEGs enriched in photosynthesis suggest that the photosynthetic system in the autotetraploid was enhanced compared with diploid during drought stress. Moreover, several genes encoding transcription factors (TFs) including GRAS, Bhlh, MYB, WRKY and NAC were induced specifically or to higher levels in the autotetraploid under drought-stress conditions, and hub genes, LOC107403632, LOC107422279, LOC107434947, LOC107412673 and LOC107432609, related to 18 up-regulated transcription factors in the autotetraploid compared with the diploid were identified. Conclusion Taken together, multiple responses contribute to the enhanced drought tolerance of autotetraploid sour jujube. This study could provide an important basis for elucidating the mechanism of tolerance variation after the polyploidization of trees.

Abstract Background Fatty liver has become a main problem that causes huge economic losses in many aquaculture modes. It is a common physiological or pathological phenomenon in aquaculture, but the causes and occurring mechanism are remaining enigmatic. Methods Each three liver samples from the control group of allogynogenetic gibel carp with normal liver and the overfeeding group with fatty liver were collected randomly for the detailed comparison of histological structure, lipid accumulation, transcriptomic profile, latent pathway identification analysis (LPIA), marker gene expression, and hepatocyte mitochondria analyses. Results Compared to normal liver, larger hepatocytes and more lipid accumulation were observed in fatty liver. Transcriptomic analysis between fatty liver and normal liver showed a totally different transcriptional trajectory. GO terms and KEGG pathways analyses revealed several enriched pathways in fatty liver, such as lipid biosynthesis, degradation accumulation, peroxidation, or metabolism and redox balance activities. LPIA identified an activated ferroptosis pathway in the fatty liver. qPCR analysis confirmed that gpx4, a negative regulator of ferroptosis, was significantly downregulated while the other three positively regulated marker genes, such as acsl4, tfr1 and gcl, were upregulated in fatty liver. Moreover, the hepatocytes of fatty liver had more condensed mitochondria and some of their outer membranes were almost ruptured. Conclusions We reveal an association between ferroptosis and fish fatty liver for the first time, suggesting that ferroptosis might be activated in liver fatty. Therefore, the current study provides a clue for future studies on fish fatty liver problems.

Abstract Background The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a devastating pathogen of many Pinus species in China. The aim of this study was to understand the interactive molecular mechanism of PWN and its host by comparing differentially expressed genes and candidate effectors from three transcriptomes of B. xylophilus at different infection stages. Results In total, 62, 69 and 46 candidate effectors were identified in three transcriptomes (2.5 h postinfection, 6, 12 and 24 h postinoculation and 6 and 15 d postinfection, respectively). In addition to uncharacterized pioneers, other candidate effectors were involved in the degradation of host tissues, suppression of host defenses, targeting plant signaling pathways, feeding and detoxification, which helped B. xylophilus survive successfully in the host. Seven candidate effectors were identified in both our study and the B. xylophilus transcriptome at 2.5 h postinfection, and one candidate effector was identified in all three transcriptomes. These common candidate effectors were upregulated at infection stages, and one of them suppressed pathogen-associated molecular pattern (PAMP) PsXEG1-triggered cell death in Nicotiana benthamiana. Conclusions The results indicated that B. xylophilus secreted various candidate effectors, and some of them continued to function throughout all infection stages. These various candidate effectors were important to B. xylophilus infection and survival, and they functioned in different ways (such as breaking down host cell walls, suppressing host defenses, promoting feeding efficiency, promoting detoxification and playing virulence functions). The present results provide valuable resources for in-depth research on the pathogenesis of B. xylophilus from the perspective of effectors.

• A series of histological differences of the testicular peritoneal sheath were found in the cutworm when compared with the silkworm during the larva to pupa metamorphosis. • Compared with the silkworm, 146 genes that were significantly up-regulated before testicular fusion in the cutworm and 139 genes that were significantly down-regulated after testicular fusion in the cutworm. 391 genes that were highly and species-specific expressed in the testis fusion stage in the cutworm. • Five transcript factors including Slforkhead, Slproline, Slcyclic, Slsilk, and SlD-ETS were screened out and they may participate in regulating testicular fusion. Spodoptera litura commonly known as the cutworm, is among the most destructive lepidopteran pests affecting over 120 plants species. The powerful destructive nature of this lepidopteran is attributable to its high reproductive capacity. The testicular fusion that occurs during metamorphosis from larvae to pupa in S.litura positively influences the reproductive success of the offspring. In contrast, Bombyx mori , the silkworm, retains separate testes throughout its life and does not undergo this fusion process. Microscopic examination reveals that during testicular fusion in S.litura , the peritoneal sheath becomes thinner and more translucent, whereas in B.mori, the analogous region thickens. The outer basement membrane in S.litura exhibits fractures, discontinuity, and uneven thickness accompanied by a significant presence of cellular secretions, large cell size, increased vesicles, liquid droplets, and a proliferation of rough endoplasmic reticulum and mitochondria. In contrast, the testicular peritoneal sheath of B.mori at comparable developmental stage exhibits minimal change. Comparative transcriptomic analysis of the testicular peritoneal sheath reveals a substantial difference in gene expression between the two species. The disparity in differential expressed genes (DEGs) is linked to an enrichment of numerous transcription factors, intracellular signaling pathways involving Ca2+ and GTPase, as well as intracellular protein transport and signaling pathways. Meanwhile, structural proteins including actin, chitin-binding proteins, membrane protein fractions, cell adhesion, extracellular matrix proteins are predominantly identified. Moreover, the study highlights the enrichment of endopeptidases, serine proteases, proteolytic enzymes and matrix metalloproteins, which may play a role in the degradation of the outer membrane. Five transcription factors- Slforkhead, Slproline, Slcyclic, Slsilk, and SlD-ETS were identified, and their expression pattern were confirmed by qRT-PCR. they are candidates for participating in the regulation of testicular fusion. Our findings underscore significant morphological and trancriptomic variation in the testicular peritoneal sheath of S.litura compared to the silkworm, with substantial changes at the transcriptomic level coinciding with testicular fusion. The research provides valuable clues for understanding the complex mechanisms underlying this unique phenomenon in insects. [ABSTRACT FROM AUTHOR]

Vicia villosa (VV) and Vicia sativa (VS) are legume forages highly valued for their excellent nitrogen fixation. However, no research has addressed the mechanisms underlying their differences in nitrogen fixation. This study employed physiological, cytological, and comparative transcriptomic approaches to elucidate the disparities in nitrogen fixation between them. Our results showed that the total amount of nitrogen fixed was 60.45% greater in VV than in VS, and the comprehensive nitrogen response performance was 94.19% greater, while the nitrogen fixation efficiency was the same. The infection zone and differentiated bacteroid proportion in mature VV root nodules were 33.76% and 19.35% greater, respectively, than those in VS. The size of the VV genome was 15.16% larger than that of the VS genome, consistent with its greater biomass. A significant enrichment of the flavonoid biosynthetic pathway was found only for VV-specific genes, among which chalcone-flavonone isomerase, caffeoyl-CoA-O-methyltransferase and stilbene synthase were extremely highly expressed. The VV-specific genes also exhibited significant enrichment in symbiotic nodulation; genes related to nodule-specific cysteine-rich peptides (NCRs) comprised 61.11% of the highly expressed genes. qRT‒PCR demonstrated that greater enrichment and expression of the dominant NCR (Unigene0004451) were associated with greater nodule bacteroid differentiation and greater nitrogen fixation in VV. Our findings suggest that the greater total nitrogen fixation of VV was attributed to its larger biomass, leading to a greater nitrogen demand and enhanced fixation physiology. This process is likely achieved by the synergistic effects of high bacteroid differentiation along with high expression of flavonoid and NCR genes. • Vicia villosa surpasses Vicia sativa in nitrogen fixation. • Comparative transcriptome analysis reveals positive selection in nodulation. • Flavonoid biosynthesis enrichment in Vicia villosa enhances symbiosis. • Enhanced bacteroid differentiation in Vicia villosa due to NCR peptides. [ABSTRACT FROM AUTHOR]

Aeromonas veronii , an opportunistic pathogen, is known to cause serious infections across various species. In our previous study, we discovered that A. veronii GL2 exhibited a virulence up to ten times greater than that of FO1. To ascertain the factors contributing to the disparity in virulence between the two strains, we conducted a comparative transcriptome analysis. This analysis reveals a significant upregulation (P < 0.05) of the ascR gene in GL2 compared with FO1. Additionally, six differentially expressed genes (DEGs) were identified within the "Bacterial secretion system" pathway (map03070), with ascR being an essential component of type III secretion system (T3SS). AscR, considered as SctR family export apparatus subunit within the T3SS, has ambiguous roles in the biological properties, gene expression profiles, virulence and colonization of A. veronii. Therefore, we constructed a mutant strain (Δ ascR) by homologous recombination. Comparative analysis with the wide-type GL2 reveals no significant differences in terms of colony morphology, growth curve, hemolytic activity and protease activity. However, significant reductions (P < 0.01) were observed in the abilities of biofilm formation and swimming mobility. No remarkable difference was noted in the lengths of flagella. The LD 50 value of Δ ascR was to be 5.15 times higher than that of GL2. Interestingly, the mRNA expression of ascC , ascD , ascJ and ascI genes in the T3SS, and mshB , mshE , mshK and mshP genes in the MSHA type pili were significantly upregulated (P < 0.05) in Δ ascR , potentially due to transcriptional compensation. Further analysis of enzymatic biomarkers revealed that Δ ascR might not destruct the recognition of innate immune response in host remarkably, but the colonization levels of A.veronii were significantly suppressed (P < 0.01) in Δ ascR group. In conclusion, the ascR gene may be a key determinant in regulating the virulence of A. veronii , and the destruction of the T3SS caused by ascR deficiency results in these notable changes. • Comparative transcriptome initially reveals the importance of ascR in T3SS. • Gene ascR regulates the biofilm formation capacity of A. veronii. • Gene ascR regulates swimming mobility except for flagella assembly. • Deletion of ascR triggers the transcriptional compensation of some genes. • Deletion of ascR weakens the colonization of A. veronii. [ABSTRACT FROM AUTHOR]

Foliar pigmentation patterns vary among plant species and growth conditions. In this study, we utilize hyperspectral imaging to assess foliar pigmentation in the bryophyte Marchantia polymorpha under nutrient stress and identify associated genetic factors. Using singular value decomposition (SVD) for feature selection, we quantitate color variations induced by deficiencies in phosphate, nitrate, magnesium, calcium, and iron. Pseudo-colored thallus images show that disrupting Mp WRKY10 causes irregular pigmentation with auronidin accumulation. Transcriptomic profiling shows that Mp WRKY10 regulates phenylpropanoid pathway enzymes and R2R3-MYB transcription factors during phosphate deficiency, with Mp MYB14 upregulation preceding pigment accumulation. Mp WRKY10 is downregulated in older, pigmented thalli under phosphate deficiency but maintained in young thalli, where it suppresses pigmentation genes. This downregulation is absent in pigmented thalli due to aging. Comparative transcriptome analysis suggests similar WRKY and MYB roles in nutrient response and pigmentation in red-leaf lettuce, alluding to conserved genetic factors controlling foliar pigmentation patterns under nutrient deficiency. [Display omitted] • A hyperspectral imaging method for foliar pigmentation in Marchantia polymorpha is developed • MpWRKY10 defines irregular pigmentation patterns under phosphate deficiency • MpWRKY10 plays a role in cooperating with R2R3-MYBs to regulate auronidin biosynthesis Krishnamoorthi et al. investigate foliar pigmentation in Marchantia polymorpha , utilizing hyperspectral imaging and singular value decomposition to assess pigmentation variations under nutrient stresses. Disruption of Mp WRKY10 leads to irregular pigmentation patterns due to auronidin accumulation, showing its central role in regulating phenylpropanoid metabolisms cooperatively with Mp MYB14 during phosphate deficiency. [ABSTRACT FROM AUTHOR]

Ustilaginoidea virens is the infectious agent responsible for rice false smut disease, which infects rice in rice-growing regions worldwide. This study aimed to investigate the antifungal effect and the inhibition of molecular mechanism of lavender essential oil (LEO) against U. virens. The antifungal effects of LEO were studied assessed by examining mycelia growth, spore germination, conidial production, mycelia dry weight, and protein content. Scanning electron microscopy showed serious impairment in the mycelial morphology of U. virens when exposed to the EC 50 concentration of LEO. In this study, comparative transcriptome methods were used to analyze the gene expression levels of U. virens under LEO stress. The results revealed that 845 genes (371 upregulated, 474 downregulated) and 1173 genes (554 upregulated, 619 downregulated) were differentially expressed in U. virens treated with LEO (CL) compared to the control samples (CK) after 4 and 8 d of treatment, respectively. Further analyses indicated that various genes related to cell wall synthesis, cell membrane synthesis, protein synthesis, and the energy metabolism pathway were significantly downregulated. These results suggest that LEO may reduce the expression of genes related to the cell wall, cell membrane, protein synthesis, and energy metabolism pathways of U. virens , thus destroying the stability and fluidity of cells and interfering with their protein synthesis and energy metabolism to achieve an antifungal effect. • Lavender essential oil (LEO) exhibited potent antifungal activity against U. virens. • LEO can destroy the surface structure of hypha. • LEO can reduce the protein content of the U. virens mycelia. • The molecular mechanism of LEO against U. virens by comparative transcriptome. • LEO showed good application potential as fungicide. [ABSTRACT FROM AUTHOR]

Various bacterial diseases have caused great economic losses to the high-density and intensive aquaculture industry; however, the pathogenic mechanism underlying the large-scale challenged to caused by many bacteria remain unclear, making the prevention and treatment of these diseases difficult. In the present study, we isolated a bacterial strain from Cyprinus carpio having a typical bacterial disease and named it Cc2021. Through subsequent morphological observations, a regression challenge, biochemical identification, and 16S rRNA gene sequence analysis, we determined Cc2021 to be Plesiomonas shigelloides. Subsequently, we comprehensively investigated the pathogenicity of P. shigelloides in C. carpio through a regression challenge and assessed the underlying the pathogenic mechanism. Mortality results revealed that P. shigelloides is highly pathogenic and infects various tissues throughout the body, resulting in edema of the liver, spleen, and body and head kidneys. Histopathological analysis revealed obvious inflammation, bleeding, and necrosis in the intestine, spleen, and head kidney. The body's immune tissues actively produce complement C3, superoxide dismutase, and lysozyme after a challenge to resist bacterial invasion. With regard to the underlying pathogenesis of P. shigelloides , comparative transcriptome analysis revealed 876 upregulated genes and 828 downregulated genes in the intestine of C. carpio after the challenge. Analysis of differentially expressed unigenes revealed the involvement of major immune pathways, particularly the TNF signaling pathway, interleukin (IL)-17 signaling pathway, and Toll-like receptor signaling pathway. The present study provides new valuable information on the immune system and defense mechanisms of P. shigelloides. [ABSTRACT FROM AUTHOR]

Opisthopappus is a major wild source of Asteraceae with resistance to cold and drought. Two species of this genus (Opisthopappus taihangensis and O. longilobus) have been employed as model systems to address the evolutionary history of perennial herb biomes in the Taihang Mountains of China. However, further studies on the adaptive divergence processes of these two species are currently impeded by the lack of genomic resources. To elucidate the molecular mechanisms involved, a comparative analysis of these two species was conducted. Among the identified transcription factors, the bHLH members were most prevalent, which exhibited significantly different expression levels in the terpenoid metabolic pathway. O. longilobus showed higher level of expression than did O. taihangensis in terms of terpenes biosynthesis and metabolism, particularly monoterpenoids and diterpenoids. Analyses of the positive selection genes (PSGs) identified from O. taihangensis and O. longilobus revealed that 1203 genes were related to adaptative divergence, which were under rapid evolution and/or have signs of positive selection. Differential expressions of PSG occurred primarily in the mitochondrial electron transport, starch degradation, secondary metabolism, as well as nucleotide synthesis and S-metabolism pathway processes. Several PSGs were obviously differentially expressed in terpenes biosynthesis that might result in the fragrances divergence between O. longilobus and O. taihangensis, which would provide insights into adaptation of the two species to different environments that characterized by sub-humid warm temperate and temperate continental monsoon climates. The comparative analysis for these two species in Opisthopappus not only revealed how the divergence occurred from molecular perspective, but also provided novel insights into how differential adaptations occurred in Taihang Mountains. [ABSTRACT FROM AUTHOR]

As the widest cultivated edible mushroom worldwide, Lentinula edodes suffers serious yield and quality losses from heat stress during growth and development, and in our previous study, exogenous 2,4-Dichlorophenoxyacetic acid (2,4-D) was found to improve the thermotolerance of L. edodes strain YS3357, but the molecular mechanism remains unclear. Here, we explored the potential protective mechanism of exogenous 2,4-D against heat stress by transcriptome analysis. 2,4-D possible improve the thermotolerance of L. edodes through regulating antioxidant genes, transcription factors, energy-provision system, membrane fluidity, and cell wall remodeling. Furthermore, 2,4-D was also found to regulate the saturation levels of fatty acids and ATP content in L. edodes mycelium under heat stress. This study proposed a regulatory network of 2,4-D in regulating L. edodes response to heat stress, providing a theoretical basis for improving L. edodes thermotolerance, and facilitating the understanding of the molecular mechanism of exogenous hormones in alleviating abiotic stress damage to macrofungi. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) accumulation in lettuce causes a large amount of yield loss during industry. Although many studies report that exogenous melatonin helps to alleviate the Cd stress of lettuce, the molecular mechanism for how plant tissue responds to Cd treatment is unclear. Herein, we applied both PacBio and Illumina techniques for Italian lettuce under different designed treatments of Cd and melatonin, aiming to reveal the potential molecular pathway of the response to Cd stress as well as the how the pre-application of exogenous melatonin affect this process. This result reveals that the root has the biggest expression pattern shift and is a more essential tissue to respond to both Cd and melatonin treatments than leaves. We reveal the molecular background of the Cd stress response in prospects of antioxidant and hormone signal transduction pathways, and we found that their functions are diverged and specifically expressed in tissues. We also found that candidate genes related to melatonin detoxify during Cd stress. Our study sheds new light for future research on how melatonin improves the cadmium resistance of lettuce and also provide valuable data for lettuce breeding. [ABSTRACT FROM AUTHOR]

Recent researches reveal that during oocyte maturation, species‐specific molecular profile exists and has important functional roles. However, molecular differences between pig (a larger animal model for human reproduction) and human mature oocytes remain unknown. Here, by comparative transcriptome analyses of single‐cell RNA‐seq data, we aimed to identify the common and unique maternal factors and associated biological processes between in vivo and in vitro matured pig oocytes, and between in vitro matured human and pig oocytes. Annotated protein‐coding mRNAs were identified in pig in vivo (11,147) and in vitro (11,997), and human in vitro (14,491) MII oocytes, respectively. For in vivo and in vitro derived pig MII oocytes, 10,551 annotated maternal mRNAs were common, mainly enriched in signalling pathways such as cell cycle, oocyte meiosis, microtubule cytoskeleton, MAPK, RNA processing/binding. Besides, in vivo (596) and in vitro (1446) pig MII‐specific mRNAs and their involved signalling pathways (in vivo: Bmp, calcium‐mediated signalling, PI3K‐Akt; in vitro: growth factor activity, JAK‐STAT, cytokine‐cytokine receptor interaction, calcium signalling pathway) were also found. As for in vitro derived human and pig MII oocytes, 10,285 annotated mRNAs were common, enriched in a variety of signalling pathways (cell cycle, oocyte meiosis, microtubule, AMPK, RNA splicing, protein serine/threonine kinase activity, etc). In vitro MII‐specific mRNAs were found for humans (4206) and pigs (1712), which were also enriched in species‐specific signalling pathways (humans: golgi‐related terms, transcription repressor and hormone activity; pigs: ATP biosynthetic process, G protein‐coupled peptide receptor activity, animoacyl‐tRNA biosynthesis), respectively. These findings improve our understanding on oocyte maturation, and also the limitations of pig model for human oocyte maturation and fertilization. [ABSTRACT FROM AUTHOR]