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Myceliophthora thermophila is a thermophilic fungus, known to produce industrially important enzymes in biorefineries. The mechanism underlying cellulase and xylanase expression in filamentous fungi is a complex regulatory network controlled by numerous transcription factors (TFs). These TFs in M. thermophila remain unclear. Here, we identified and characterised a novel cellulase and xylanase regulator MtFKH1 in M. thermophila through comparative transcriptomic and genetic analyses. Five of the eight potential TFs, which showed differential expression levels when grown on Avicel and glucose, were successfully deleted using the newly designed CRISPR/Cas9 system. This system identified the forkhead TF MtFKH1. The disruption of Mtfkh1 elevated the cellulolytic and xylanolytic enzyme activities, whereas the overexpression of Mtfkh1 led to considerable decrease in cellulase and xylanase production in M. thermophila cultivated on Avicel. The loss of Mtfkh1 also exhibited an impairment in sporulation in M. thermophila. Real-time quantitative reverse transcription PCR (RT-qPCR) and the electrophoretic mobility shift assays (EMSAs) demonstrated that MtFKH1 regulates the gene expression and specifically bind to the promoter regions of genes encoding β-glucosidase (bgl1 / MYCTH_66804), cellobiohydrolase (cbh1 / MYCTH_109566), and xylanase (xyn1 / MYCTH_112050), respectively. Furthermore, DNase I footprinting analysis identified binding motif of MtFKH1 in the upstream region of Mtbgl1 , with strongest binding affinity. Finally, transcriptomic profiling and Gene Ontology (GO) enrichment analyses of Mtfkh1 deletion mutant revealed that the regulon of MtFKH1 were significantly prevalent in hydrolase activity (acting on glycosyl bonds), polysaccharide binding, and carbohydrate metabolic process functional categories. These findings expand our knowledge on how forkhead transcription factor regulates lignocellulose degradation and provide a novel target for engineering of fungal cell factories with the hyperproduction of cellulase and xylanase. [ABSTRACT FROM AUTHOR]

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]

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]

As the most important cultural crustacean species worldwide, studies about Pacific white shrimp (Litopenaeus vannamei) have received more attention. It has been well-documented that various pathogens could infect L. vannamei , resulting in huge economic losses. The studies about the responding mechanism of L. vannamei to sole pathogens such as Vibrio parahaemolyticus and white spot virus (WSSV) have been extensively reported, while the studies about the differently responding mechanisms remain unclear. In the present study, we identified the differently expressed genes (DEGs) of L. vannamei hemocytes post V. parahaemolyticus and WSSV infection with RNA-seq technology and compared the DEGs between the two groups. The results showed 2672 DEGs post the V. parahaemolyticus challenge (1079 up-regulated and 1593 down-regulated genes), while 1146 DEGs post the WSSV challenge (1067 up-regulated and 513 down-regulated genes). In addition, we screened the genes that simultaneously respond to WSSV and V. parahaemolyticus (434), solely respond to WSSV (1146), and V. parahaemolyticus challenge (2238), respectively. Six DEGs involved in innate immunity were quantified to validate the RNA-seq results, and the results confirmed the high consistency of both methods. Furthermore, we found plenty of innate immunity-related genes that responded to V. parahaemolyticus and WSSV infection, including pattern recognition receptors (PRRs), the proPO activating system, antimicrobial peptides (AMPs), and other immunity-related proteins. The results revealed that they were differently expressed after different pathogen challenges, demonstrating the complex and specific recognition systems involved in defending against the invasion of different pathogens in the environment. The present study improved our understanding of the molecular response of hemocytes of L. vannamei to V. parahaemolyticus and WSSV stimulation. [Display omitted] • This is the first report exploring different responding mechanisms underlying Vibrio and WSSV infection in hemocytes. • The DEGs responding to Vibrio parahaemolyticus and WSSV exist huge difference. • The expression level of some genes shows opposite trend post Vibrio parahaemolyticus and WSSV. [ABSTRACT FROM AUTHOR]

The elevated salinity in freshwater causes a serious threat to the survival and reproduction of freshwater organisms. The effect of salinity on embryonic development of freshwater turtles is little known. In this study, we investigated the embryonic morphology and underlining mechanism of red-eared slider (Trachemys scripta elegans) in different salinities incubated environment (2.5 ppt and 5 ppt). Results showed that salinity caused various forms of malformed embryos, including brain hypoplasia, eye defects, skeletal dysplasia, deformities of carapace, plastron, limb in the embryo. Severely, salinity could lead to embryos decease. Transcriptome analysis showed that differentially expressed genes induced by salinity primarily enriched in development pathways, metabolism pathways, disease pathways as well as cell processes through KEGG enrichment analysis. In addition, in early and middle embryonic developmental stages, the mRNA expression of apoptotic genes (p38 and bax) significantly increased, whereas anti-apoptotic gene bcl-2 decreased in salinities incubated environment. These findings demonstrated that salinity inhibited the process of embryonic development and damaged organogenesis of turtles through promoting apoptotic pathways. [Display omitted] • Salinity stress resulted in aberrant morphology and embryonic mortality of red-eared turtle embryos. • Salinity exposure influenced the pathways associated with embryonic development of red-eared turtles. • Salinity stress led to notable variations in the expression of apoptotic genes. [ABSTRACT FROM AUTHOR]

Albinism is a genetically inherited condition that is caused by a series of genetic abnormalities leading to a reduction in melanin production. Russian sturgeon is one of the most valuable freshwater fish species worldwide, and albino individuals have been found in fish farms. Due to its complicated genome and scarce genome-wide genetic resources, the underlying molecular basis of albinism in Russian sturgeon is unknown. In the present study, we first generated transcriptome profile of Acipenser gueldenstaedtii using pooled tissues, which provided reliable reference sequences for future molecular genetic studies. A total of 369,441 contigs were assembled, corresponding to 32,965 unique genes. A comparative analysis of the transcripts from the skin of albino and wildtype individuals was conducted afterwards. A total of 785 unique genes were differentially expressed, including the upregulation of 385 genes and the downregulation of 400 genes in albino individuals. The expression pattern of 16 selected differentially expressed genes was validated using qRT-PCR. Additional annotation, GO enrichment analysis and gene pathway analysis indicated that the melanogenesis pathway may be interrupted in albinism. Eight potential causative genes that were highly likely to be responsible for sturgeon albinism were identified, including Dct , Tyrp1b , Slc45a2 , Ctns , Pmela , Pmelb , Cd63 , and Bloc1s3 , which were found to be significantly down-regulated in albino Russian sturgeon. Moreover, a sliding window analysis of the ratio of nonsynonymous to synonymous nucleotide substitution rates (Ka/Ks) ratios indicated that seven out of the eight genes underwent positive selection during evolution. Our results provide a valuable basis for understanding the molecular mechanism of albinism in fish species and will facilitate future genetic selection and breeding of sturgeon with market-favored traits in aquaculture. [ABSTRACT FROM AUTHOR]

Abstract The kuruma shrimp Marsupenaeus japonicus is an economically important crustacean that is widely distributed throughout the Indo-West Pacific. However, M. japonicus exhibits relatively poor thermotolerance properties and frequently suffers from mass mortality during the hot summer months in aquaculture systems. Herein, we performed a comparative transcriptome analysis of M. japonicus in response to heat stress, focusing on immune responses, heat shock proteins, antioxidant systems and metabolism alterations under heat stress. The results revealed that M. japonicus generated adaptive responses to maintain physiological homeostasis under heat stress via the transcriptional up-regulation of heat shock proteins and antioxidant enzymes, enhancement of fatty acid metabolism. However, acute and prolonged exposure to heat stress resulted in the continually decreased expression of immune molecules and led to the repression of glycometabolism, the tricarboxylic acid cycle and the respiratory chain. This study provides a systematic overview of the M. japonicus heat stress response and elucidates potential molecular mechanisms underlying this phenomenon and summer mortality syndrome in this species, which is beneficial for proposing effective strategies to address summer mortality syndrome and promote kuruma shrimp production. Highlights • A comparative transcriptome analysis of Marsupenaeus japonicus in response to heat stress was performed for the first time. • This study elucidated the molecular mechanisms of the heat stress response and summer mortality syndrome in M. japonicus. • The tremendous data obtained from RNA-Seq provide valuable genomic resources for the genetic improvement of M. japonicus. [ABSTRACT FROM AUTHOR]

α -linolenic acid (ALA) deficiency and a skewed ω6: ω3 fatty acid ratio in the diet are thought to be a major cause for the high incidence of cardiovascular, inflammatory, and autoimmune diseases. Recent years, tree peony ( Paeonia suffruticosa Andr.) with the high proportion of ALA (more than 45% in seed oil) is widely concerned. However, the underlying accumulation mechanism of the ALA in tree peony seeds remains unknown. In this study, comparative transcriptome analysis was performed between two cultivars (‘Saiguifei’ and ‘Jingshenhuanfa’) with different ALA contents. The analysis of the metabolic enzymes associated with ALA biosynthesis and temporal accumulation patterns of unsaturated fatty acids demonstrated the importance of microsomal ω-3 fatty acid desaturase 3 (FAD3). Moreover, PsFAD3 gene was identified from tree peony seeds, which was located in endoplasmic reticulum and the expression levels of PsFAD3 were consistent with ALA accumulation patterns in seeds. Heterologous expression in Saccharomyces cerevisiae and Arabidopsis thaliana confirmed that the isolated PsFAD3 protein could catalyze ALA synthesis. These results indicated that PsFAD3 was involved in the synthesis of ALA in seeds and could be exploited by the genetic breeding of new cultivars with high ALA content in tree peony as well as other potential crops. [ABSTRACT FROM AUTHOR]

Saperda populnea is a serious pest of poplar and willow trees in the Palaearctic region, causing extensive damage to forests and the lumber industry. Until recently, there is no safe and effective chemical method to control this pest due to the lack of sufficient knowledge on the molecular basis of its olfactory genes, moreover, the evolutionary history of the olfactory gene family in subfamily Lamiinae is still fully unknown. Our RNA sequencing of the antennae of S . populnea identified 43 odorant binding proteins (OBPs), 15 chemosensory proteins (CSPs), 56 odorant receptors (ORs) and 24 inotropic receptors (IRs) in S . populnea . The RT-PCR results showed several genes were expressed in a sex specific manner, suggesting that these genes might play key role in their olfactory-sensing and sex-related behaviors. Further evolutionary studies were performed on these olfactory genes, overall comparison of the Ka/Ks values of orthologous genes in S . populnea and two other Lamiinae species showed three main conclusions: 1. olfactory genes have evolved more rapidly than the non-olfactory genes in the tested long horn beetles; 2. the IR gene family are under a strong purifying selection; 3. the OBPs of Monochamus alternatus evolved more rapidly than the other two species, which is speculated to be correlated with differentiation of selective pressure in different geographic origins. Detailed evolutionary studies on each olfactory genes showed that several OBPs and ORs are under significantly purifying/relaxed selective pressure, and several positive selection sites were also detected, modeling of SpopOR14 and SpopOBP4/5 showed that most of the positive selection sites were distributed at the N-terminus of SpopOR14, while the positive selection sites in SpopOBP4/5 were located in H-bond donors, results suggest that these sites are more likely to be linked with the selectivity of modeled olfactory genes. The research provided a better understanding of the molecular basis and evolutionary history of the olfactory genes in Lamiinae, through elaborating the mechanism whereby amino structural evolution affects specific variants in OBPs and ORs. [ABSTRACT FROM AUTHOR]

Alvinocaris longirostris Kikuchi and Ohta, 1995 is one of the few species co-distributed in deep-sea hydrothermal vent and cold seep environments. We performed the transcriptome analysis for A. longirostris and identified differentially expressed genes (DEGs) between samples from the Iheya North hydrothermal vent (HV) and a methane seep in the South China Sea (MS). From the 57,801 annotated unigenes, multi-copies of enzyme family members for eliminating toxic xenobiotics were isolated and seven putatively duplicated gene clusters of cytochrome P450s were discovered, which may contribute to adaptation to the harsh conditions. Eight single amino acid substitutions of a Rhodopsin gene with low expression in two deep-sea alvinocaridid species were positively selected when compared with shallow water shrimps, which may be the result of adaptation to the dim-light environment in deep sea. 408 DEGs were identified with 53 and 355 up-regulated in HV and MS, respectively. Various genes associated with sulfur metabolism, detoxification and mitochondria were included, revealing different mechanisms of adaptation to the two types of extreme environments. All results are expected to serve as important basis for the further study. [ABSTRACT FROM AUTHOR]

Pyropia haitanensis farms in South China often suffer from sustained high temperatures in autumn, which is the early seeding period, resulting in disease, premature senility, and eventual decay, ultimately leading to a substantial reduction in yield. However, the molecular mechanisms underlying the response to high temperature stress in P. haitanensis remain unknown. In the present study, we used the Illumina sequencing platform to examine the transcriptional profiles of heat-tolerant (THT) and heat-sensitive (WHT) P. haitanensis strains exposed to different durations of high temperature stress. THT exhibited more differentially expressed genes and greater fold-changes in transcripts under sustained temperature stress, suggesting that this strain is better able to increase transcriptional regulation in response to high temperature stress than WHT. Furthermore, heat stress induced different expression patterns in the thalli of the two strains. THT was able to maintain or increase the activities of energy metabolism, antioxidant systems, and phosphatidylinositol signal transduction to resist heat stress, while these processes were dramatically reduced in WHT, resulting in the thalli being unable to survive under sustained high temperatures. The present data provide a better understanding of the mechanisms underlying the response of P. haitanensis to high temperature stress, which may facilitate the development of technologies and breeding strategies for improving thermotolerance in Pyropia . [ABSTRACT FROM AUTHOR]

The post-transcriptional regulator CsrA regulates multiple unrelated processes such as central carbon metabolism, motility, biofilm formation and bacterial virulence in different bacteria. However, regulation by CsrA in enterohemorrhagic Escherichia coli (EHEC) O157:H7 is still largely unknown. In this study, we performed a detailed analysis of gene expression differences between the EHEC O157:H7 wild-type strain and a corresponding csrA::kan mutant using RNA-seq technology. Genes whose expression was affected by CsrA were identified and grouped into different clusters of orthologous group categories. Genes located in the locus of enterocyte effacement (LEE) pathogenicity island were significantly upregulated, whereas expression of flagella-related genes was significantly reduced in the csrA::kan mutant. Subsequent bacterial adherence and motility assays showed that inactivation of CsrA in EHEC O157:H7 resulted in a significant increase in bacterial adherence to host epithelial cells, with a concomitant loss of swimming motility on semi-solid agar plates. Furthermore, we also found that CsrA regulates genes not previously identified in other bacterial species, including genes encoding cytochrome oxidases and those required for nitrogen metabolism. Our results provide essential insight into the regulatory function of CsrA. [ABSTRACT FROM AUTHOR]

Quadrastichus mendeli Kim is one of the most important parasitoids of Leptocybe invasa Fisher et La Salle, which is an invasive gall-making pest in eucalyptus plantations in the world. Gall-inducing insects live within plant tissues and induce tumor-like growths that provide the insects with food, shelter, and protection from natural enemies. Empirical evidences showed that sensory genes play a key role in the host location of parasitoids. So far, what kind of sensory genes regulate parasitoids to locate gall-inducing insects has not been uncovered. In this study, sensory genes in the antenna and abdomen of Q. mendeli were studied using high-throughput sequencing. In total, 181,543 contigs was obtained from the antenna and abdomen transcriptome of Q. mendeli. The major sensory genes (chemosensory proteins, CSPs; gustatory receptors, GRs; ionotropic receptors, IRs; odorant binding proteins, OBPs; odorant receptors, ORs; and sensory neuron membrane proteins, SNMPs) were identified, and phylogenetic analyses were performed with these genes from Q. mendeli and other model insect species. The gene co-expression network constructed by WGCNA method is robust and reliable. There were 10,314 differentially expressed genes (DEGs), and among them, 99 genes were DEGs. A comprehensive sequence resource with desirable quality was built by comparative transcriptome of the antenna and abdomen of Q. mendeli , enriching the genomic platform of Q. mendeli. [Display omitted] • Quadrastichus mendeli is a parasitoid of gall-making pest Leptocybe invasa described in 2008. • Q. mendeli has the potential to be a biological control agent for L. invasa. • Comparative transcriptome of the antenna and abdomen of Q. mendeli enriching the genomic platform of Q. mendeli. • A detailed description of sensory genes from the antenna and abdomen of Q. mendeli. [ABSTRACT FROM AUTHOR]

Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is the first line of defense in plant disease resistance. However, the molecular mechanisms of plant PTI vary across species, making it challenging to identify a core set of trait-associated genes. This study aimed to investigate key factors that influence PTI and identify the core molecular network in Sorghum bicolor , a C4 plant. We performed comprehensive weighted gene co-expression network analysis and temporal expression analysis of large-scale transcriptome data from various sorghum cultivars under different PAMP treatments. Our results revealed that the type of PAMP had a stronger influence on the PTI network than did the sorghum cultivar. Following PAMP treatment, 30 genes with stable downregulated expression and 158 genes with stable upregulated expression were identified, including genes encoding potential pattern recognition receptors whose expression was upregulated within 1 h of treatment. PAMP treatment altered the expression of resistance-related, signaling, salt-sensitive, heavy metal-related, and transporter genes. These findings provide novel insights into the core genes involved in plant PTI and are expected to facilitate the identification and application of resistance genes in plant breeding studies. • The sorghum immune response is influenced by PAMP type at the transcriptome level. • Core genes were identified using WGCNA and treatment time expression analyses. • The main PAMP-induced immune response time was 3–6 h. • PAMPs induced stable upregulation of 158 genes and downregulation of 30 genes. • Gene expression of pattern recognition receptors was upregulated within 1 h. [ABSTRACT FROM AUTHOR]

Catfish (Siluriformes) are one of the most diverse vertebrate orders and are characterized by whisker-like barbels, which are important sensory organs in most of teleosts. However, their specific biological functions are still unclear. Red-tail catfish (Hemibagrus wyckioides) is well-known catfish species with four pairs of barbels, of which the maxillary barbels reach two-thirds of the body length. In this study, a 776.58 Mb high-quality chromosome-level genome was assembled into 29 chromosomes. Comparative genome data indicated that the barbeled regeneration gene ccl33 has expanded into 11 tandemly duplicated copies. Transcriptome data revealed the functional differentiation of different barbels and suggested that the maxillary barbel might be necessary for water temperature perception. Taste receptor genes were also characterized in teleosts with different food habits. Selection pressures were revealed to affect the sugar-based solute transport domain of the sweet taste receptor gene t1r2 in carnivorous fishes. In addition, the bitter taste receptor gene t2r200 was found to be lost from the genomes of four catfish species. Therefore, our study provides a genomic foundation for understanding the regeneration and functional differentiation of barbels in red-tail catfish and also reveals novel insights into the feeding evolution of fish species with different feeding habits. • A high-quality reference genome sequence with complete annotation in red-tail catfish was assembled in this study. • Genome evolution among the different catfish genomes was explored. • Barbeled regeneration gene ccl33 was found to be tandemly duplicated in red-tail catfish genome. • This research revealed functional differentiation of four pairs of barbels. • Two taste receptor genes t1r2 and t2r were characterized in different food habit teleosts. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a heavy metal contaminant and can be toxic to environment. What's more, Selenium (Se) protects organism as heavy metal antagonist. The present study aimed to investigate whether inorganic (Na 2 SeO 3) or organic (L-SeMc) Se have an effect on the Cd bioaccumulation, antioxidant and immunity of the mud crab (Scylla paramamosain) under Cd exposure. The study showed that the concentration of Cd in hepatopancreas under Cd exposure was higher than the inorganic or organic Se group (P < 0.05), notably, Cd concentration of hepatopancreas in organic Se treatment is less than that in inorganic Se treatment (P < 0.05). Furthermore, this study analyzed 28 gene expression about antioxidant and immune from transcriptome, the result indicated that L-SeMc (organic Se) can reduced intracellular ROS production and oxidative damage. Furthermore, apoptosis was enhanced after Cd exposure, but Se could protect against apoptosis via expression of cathepsin B. Consequently, Organic Se may have a better effect than inorganic Se on reducing Cd toxicity. This study could provide the molecular basis that Se might alleviate Cd toxicity and increases the understanding of the environmental contaminant on crustaceans. [Display omitted] • Se reduce the Cd concentration in the hepatopancreas. • GO and KEGG pathways were significantly enriched after Cd and Se exposure. • 26 immune-related DEGs were studied. • Organic selenium may have a better effect than inorganic Se on reducing Cd toxicity. [ABSTRACT FROM AUTHOR]

In this work, a Cellvibrio pealriver- microalga co-cultivation mode was used to promote the growths of four microalgae by using xylan as feedstock. After 12 days of cultivation, the biomass concentrations of Chlorella sacchrarophila , Chlorella pyrenoidosa and Chlamydomonas reinhardtii in co-cultivation were equal to those in mixotrophic growth on glucose, and the Dunaliella was about 1.6-fold higher than that on glucose. The comparative transcriptomes analysis demonstrated that the xylose and xylan hydrolysates were catalyzed to some active substrates by C. pealriver via some functional enzymes; these active substrates are possibly responsible for the promotion of microalgal growth. This C. pealriver- microalga co-cultivation mode is a potential method to produce low-cost microalgal biodiesel by using hemicellulose as feedstock. [ABSTRACT FROM AUTHOR]

Downy mildew (DM), caused by oomycete Plasmopara viticola (Pv), can lead to severe damage to Vitis vinifera grapevines. Vitis amurensis has generally been regarded as a DM resistant species. However, when V. amurensis ‘Shuanghong’ were inoculated with Pv strains ‘ZJ-1-1’ and ‘JL-7-2’, the former led to obvious DM symptoms (compatible), while the latter did not develop any DM symptoms but exhibited necrosis (incompatible). In order to underlie molecular mechanism in DM resistance, mRNA-seq based expression profiling of ‘Shuanghong’ was compared at 12, 24, 48 and 72 h post inoculation (hpi) with these two strains. Specific genes and their corresponding pathways responsible for incompatible interaction were extracted by comparing with compatible interaction. In the incompatible interaction, 37 resistance ( R ) genes were more expressed at the early stage of infection (12 hpi). Similarly, genes involved in defense signaling, including MAPK. ROS/NO, SA, JA, ET and ABA pathways, and genes associated with defense-related metabolites synthesis, such as pathogenesis-related genes and phenylpropanoids/stilbenoids/flavonoids biosynthesizing genes, were also activated mainly during the early stages of infection. On the other hand, Ca 2+ signaling and primary metabolism, such as photosynthesis and fatty acid synthesis, were more repressed after ‘JL-7-2’ challenge. Further quantification of some key defense-related factors, including phytohormones, phytoalexins and ROS, generally showed much more accumulation during the incompatible interaction, indicating their important roles in DM defense. In addition, a total of 43 and 52 RxLR effectors were detected during ‘JL-7-2’ and ‘ZJ-1-1’ infection processes, respectively. [ABSTRACT FROM AUTHOR]

Lentinula edodes is an important candidate for heavy metal mycoremediation. This study explored the molecular mechanism of cadmium (Cd) tolerance differentiation of L. edodes through comparative mRNA and milRNA analyses of two strains, YS45 (Cd sensitive) and YS119 (Cd tolerant). Results showed the emergence of more possible protein aggregates in YS45 than in YS119 under Cd stress. The number of differentially expressed genes (DEGs) and milRNAs (DEMs) was identified as 2036 and 370 as well as five and three in YS45 and YS119, respectively. Comparison of DEGs and DEMs between the two strains revealed that genes and milRNAs involved in cell wall remodeling, transport, heavy metal chelation, lipid and carbohydrate metabolism, transcription regulation, redox homeostasis, proteolysis, signaling, DNA repair, cell cycle, may play important roles in Cd stress response, and their different expression patterns, especially those associated with proteolysis and carbohydrate metabolism, might lead to Cd tolerance differentiation between the two strains. The function of the α-amylase gene LeAmy in enhancing Cd tolerance in L. edodes was further verified by overexpression. This study has shed light on the molecular mechanism of Cd tolerance differentiation in L. edodes , and laid a foundation for breeding elite strains for heavy metal mycoremediation. [Display omitted] • Mechanism of Cd tolerance differentiation was revealed by mRNA and milRNA analyses. • It is the first to disclose functions of milRNA in Cd response in macrofungi. • An α-amylase gene, LeAmy , was verified to increase Cd tolerance in shiitake. [ABSTRACT FROM AUTHOR]

As one of the most valuable maricultured species, spotted knifejaw (Oplegnathus punctatus) has high popularity in eastern Asia. In recent years, diseases caused by Vibrio harveyi have brought huge economic losses in spotted knifejaw industry. To better understand the molecular mechanisms of immune response about V. harveyi resistance in spotted knifejaw, a comparative transcriptome analysis was performed on spleen tissues at five different time points post-infection (0, 12, 24, 48 and 72 hpi). A total of 4279 differentially expressed genes (DEGs) were identified. KEGG pathways analysis showed that multiple immune-related pathways were significant regulated, including Toll-like receptor signaling pathway, ECM-receptor interaction pathway, cytokine-cytokine receptor interaction pathway and hematopoietic cell lineage pathway. Weighted gene co-expression network analysis showed that several immune-related pathways of the highest correlation with 12 hpi (cor = 0.89, P = 7e-06) were significantly enriched. In addition, 12 hpi was a turning point for 7 gene clusters out of 9 that were divided according to gene expression patterns. Therefore, we speculated that 12 hpi might be a very critical time point for spotted knifejaw against V. harveyi infection. Additionally, qRT-PCR was carried out to validate the expressions of 12 DEGs. This study provided the first systematical transcriptome analysis of spotted knifejaw against V. harveyi. The results could help us better understand the dynamic immune responses of spotted knifejaw against bacterial infection, and provide useful information for antibacterial defense in spotted knifejaw industry as well. • 4279 differentially expressed genes were identified in the spleen of spotted knifejaw infected with Vibrio harveyi. • 12 hpi might be a critical time point for spotted knifejaw against V. harveyi infection. • Multiple immune-related pathways were enriched in the infected spotted knifejaw. • Several cytokines and chemokines were up-regulated by bacterial infection. [ABSTRACT FROM AUTHOR]

Production of microbial biomass, microbial cell properties, and biological function significantly vary with hydrophobic organic compound (HOC) types used by microorganisms. However, metabolic responses underlying such variations are unclear. Herein, we identified and selected a biodemulsifier, Dietzia natronolimnaea S-XJ-1, as a model bacterium utilizing different HOCs, and performed comparative transcriptomic analyses to investigate metabolic responses induced by alkanes and fatty acid esters. As compared to the rapeseed oil-cultured S-XJ-1, the liquid paraffin-cultured S-XJ-1 possessed lower biomass production and higher cell-surface hydrophobicity. For the latter, transcriptomic data revealed the upregulation of ATP-binding cassette transporters, the downregulation of transporters for hydrophilic nutrients and cell division genes such as ftsZ and ftsE , indicating higher energy consumption, lower nutrient availability, and limited cell division, respectively. These metabolic responses can be responsible for lower biomass production in liquid paraffin-cultured S-XJ-1. Moreover, the upregulation of genes involved in the biosynthesis of surface proteins, poly-L-glutamine layer, and mycolic acids, such as secD , glnA , pks13 , and fadD32 , enhanced cell-surface hydrophobicity and the biodemulsifying activity of liquid paraffin-cultured S-XJ-1. The key genes and metabolic pathways identified in this study can direct research toward a more effective biodemulsifier design and understanding complex metabolic response profiles induced by different HOCs. • Comparative transcriptome of S-XJ-1 cultivated with alkanes and fatty acid esters. • Transmembrane transport and alkane initial oxidation were key influencing factors. • Oxidative stress lowers biomass production but elevates cell-surface hydrophobicity. [ABSTRACT FROM AUTHOR]

Highlights: [•] The small RNAs contained in vesicles originate from multiple sources. [•] Results revealed differences in the variety of small RNAs between parasite stages. [•] The data call attention to the potential regulatory functions that these RNAs might play. [Copyright &y& Elsevier]

Mangroves are a group of unique plants anchoring in and well adapting to the extreme intertidal environment with high salinity, hypoxia and high temperature and ultraviolet (UV) radiation. Sonneratia caseolaris is a major mangrove tree widely distributed across the West-Indo Pacific region, however the genetic mechanisms of its adaptive evolution are still unclear. In the present study, we performed comparative transcriptome analyses between S. caseolaris and its two non-mangrove relatives, Trapa bispinosa and Duabanga grandiflora , to better understand the evolutionary adaptation of S. caseolaris . We obtained 39.92, 69.96 and 47.78 million high-quality paired-end reads using the Illumina platform and de novo assembled them into 47,954, 73,284 and 66,459 unigenes with low redundancy and high coverage. Of them, 20,181, 28,657 and 25,244 unigenes were successfully assigned to level-2 Gene Ontology (GO) terms, and we found the distribution of GO terms were similar among the three species. Approximate 56% unigenes were involved in “response to stimulus” in all three species. Furthermore, we identified 23 unigenes under positive selection in S. caseolaris , which may be crucial for adaptation of this mangrove species to the extreme intertidal environment. [ABSTRACT FROM AUTHOR]

Desmodesmus sp.YT rich in bioactive substances exhibited impressive tolerance to various environmental conditions. To investigate the metabolism transformation influenced by salt stress in Desmodesmus sp.YT, biochemical compositions and comparative transcriptome were thoroughly explored in this research. Results showed that normal treatment (0‰ salinity) was beneficial for the production of biomass (up to 1.87 times) and protein (up to 1.46 times), compared with salt treatment. Furthermore, differentially expressed genes analysis revealed that vital genes involved in photosynthesis (light-harvesting complexs, LHCs ; photosystem II oxygen-evolving enhancer proteins, Psbs), C3 photosynthetic pathway (fructose-bisphosphate aldolase, ALDO ; fructose-1,6-bisphosphatase, PFK ; phosphoglycerate kinase, PGK) and chlorophyll synthesis (coproporphyrinogen III oxidase, CPOX ; porphobilinogen synthase, HemB) were significantly up-regulated in 0‰ salinity, leading to enhanced cell growth. Interestingly, salt stress stimulated the expression of cellulose synthase catalytic subunit A2 (CesA2) and starch synthase (GLGA), increasing the biosynthesis of cellulose (up to 3.23 times) and starch (up to 1.05 times). Results showed that Desmodesmus sp.YT cultured at freshwater could be applied as feed additives while microalgae grown in seawater had the potential for biofuel production for further mass cultivation. [Display omitted] • 0‰ salinity benefits protein yield in Desmodesmus sp. as potential nutrient source. • Improved chlorophyll synthesis under freshwater enhances the Desmodesmus sp. growth. • Salt stress improved membrane fluidity by enhancing PUFAs accumulation. • Salt stress stimulated the expression of CesA2 promoting the cellulose synthesis. [ABSTRACT FROM AUTHOR]

The hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) named Hulong grouper is a vital species variety in the grouper farming industry. During the breeding process, the hybrid grouper gradually showed the skin color variation phenomenon, including normal (N), white (W), secondary color (SC), and yellow (Y). We utilized a comparative transcriptome analysis approach via high throughput sequencing in different skin color grouper groups to understand the underlying molecular mechanism. Quantitative RT-PCR validated 20 differentially expressed genes consistent with the RNA-seq trend, indicating that our sequencing results are stable and reliable. Four skin transcriptomes were compared pairwise. The results revealed that four immune response-related genes (tlr4 , ddit4 , gpcr , and hsd3b) were the common DEGs in the different groups suggesting that there were some relations between pigmentation variance and immune difference. Therefore, further analysis of SOD, CAT, complement C3 and C4, and other immune-related genes showed that the normal group's immune status and anti-oxidative stress ability are stronger than other skin color groups. Moreover, the KEGG pathway analysis results showed that some DEGs were associated with the MAPK signal pathway, so we compared the proteic level differences of erk1/2 , p38mapk , and jnk1 among different skin-color groups. We found the MAPK is a potential pathway involved in fish skin color regulation and plays an essential role in physiological and biochemical processes. In addition, expression pattern analysis showed that the mRNA expression of most melanin synthesis-related genes have the highest level in normal color individuals, consistent with the section analysis. These results shed light on the regulatory mechanism of different skin colors transformation in hybrid Hulong grouper. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values. • ERK1/2、JNK1 and P38MAPK have different phosphorylation level in the skin of different color. • Skin color is a reference signal when judging whether the hybrid grouper is in a sub-healthy state. • MAPK is a potential bridge between immune regulation and skin-color changes. [ABSTRACT FROM AUTHOR]

The Asian yellow pond turtle (Mauremys mutica) displays temperature-dependent sex determination (TSD), in which incubation temperature during embryonic development determines the sexual fate of the individual. However, the mechanism of the sex determination/differentiation of Mauremys mutica remains a mystery. Here, we first analyzed the temperature-specific gonadal transcriptomes of Mauremys mutica prior to gonad formation and gonads during the thermosensitive period. We uncovered a list of candidates that respond to temperature stimuli enriched in several categories, such as heat shock protein family members dnajb6a , dnaja4 , hspa8 and hsp90aa1 , temperature sensor genes mmp17 and mmp28 , and putative novel temperature-responsive genes tmco6 , gria3 and eif3f. Notably, striking differences were identified in the expression profiles of genes underlying sexual development, such as tex15 , insr , igf1r , cirbp , esr1 , dmrt2 and Serpinh1. Moreover, we analyzed the similarity and divergence of the timecourse of gene expression among Mauremys mutica and two other reported TSD turtles (Trachemys scripta and Chrysemys picta). The shared genes revealed the common gonad-specific regulatory mechanisms existing in these three TSD turtles that initiate their sexual development. Therefore, our findings could provide basic data to elucidate the mechanisms of sex determination/differentiation of M. mutica , even contributing to further understanding of these mechanisms in other TSD turtles. [Display omitted] • A list of candidates genes that respond to temperature stimuli were identified in Mauremys mutica. • Striking differences were identified in the expression profiles of genes underlying sexual development of Mauremys mutica. • Eight shared genes associate with common gonad-specific regulatory mechanisms were identified in the three TSD turtles. [ABSTRACT FROM AUTHOR]

The southern tip of South America and Antarctica are particularly interesting due to many genera and also species currently sharing between both areas. The genus Nacella (Patellogastropoda: Nacellidae) is distributed in different regions of South America and Antarctica living preferentially on rocks and boulders and grazing on algae, diatoms and bacterial films. We described the transcriptomes of three Nacella species, Nacella concinna (Strebel, 1908), inhabiting the Antarctic Peninsula; Nacella magallanica (Gmelin, 1791), from Patagonia and Nacella clypeater (Lesson, 1831), from central Chile. In total, we obtained over 20,000 contigs with an average length of 583 bp. Homologous protein coding genes (PCGs) for mitochondrial genome of the three species were characterized and a database of molecular markers was also generated. This study represents the first publicly available report on pyrosequencing data for patellogastropod species, and provides an important comparative resource for studies in ecophysiology and evolutionary adaptation in marine invertebrate species. [ABSTRACT FROM AUTHOR]

• Growth and photosynthesis of S. fusiforme seedling were inhibited by K. mikimotoi. • Co-cultivated with K. mikimotoi led to the leaves of S. fusiforme seedling rot. • More epidemic cells of S. fusiforme seedling decomposed with prolongation of the co-cultivation time. • Transcripts of the photosynthesis-related genes differentially expressed during the co-cultivation. The impacts of harmful algal blooms (HABs) on macrophytes have rarely been studied, although HABs are currently considered one of the major worldwide marine environmental threats. In this study, we incorporated photophysiology experimental data with paraffin-embedded section and transcriptome analysis of S. fusiforme to explore the effects of dense K. mikimotoi culture on the growth, photosynthetic activities, and leaf microstructure of S. fusiforme , as well as the expression of the genes related to its photosynthesis. The results showed that the fresh weight, Chl a contents, apparent photosynthetic efficiency (α) and relative electron transfer rate (rETR max) of S. fusiforme seedlings cultivated for ten days with K. mikimotoi decreased by 53.60 %, 13.48 %, 6.30 % and 36.51 %, as compared with those cultivated without K. mikimotoi. The leaves of the S. fusiforme seedlings began to rot and detach from the stems after a week of cultivation with K. mikimotoi , and additional epidermic cells decomposed with prolonged exposure to the dinoflagellate. Transcripts of the genes related to photosystem reaction center subunits and photosynthesis antenna proteins were expressed differentially during the cultivation with K. mikimotoi , consistent with changes in the photosynthesis of S. fusiforme seedlings. These combined results indicate that the main mechanism for resistance to HABs is the formation of epidermis by a layer of tightly arranged cylindrical cells combined with differential expression of the photosynthesis-related genes. [ABSTRACT FROM AUTHOR]

High CO 2 acclimation for microalgae has attracted large research attention owing to the usefulness of microalgae in bio-sequestration of CO 2 from the emission source. In this study, one high CO 2 tolerant (LAMB 31) and non-tolerant (LAMB 122) Chlorella sp. strains were transferred from air to 40% CO 2 , during which four time points were chosen for comparative transcriptome analysis. Gene changes started in the lag phase (T1) of population growth with more genes (7889) upregulated in LAMB 31 than in LAMB 122 (1092). Further function enrichments indicated: In LAMB 31, up-regulation of genes in cyclic electron transportation, F-type ATPase and Calvin cycle were associated with the enhancement of carbon fixation abilities; upregulation of genes in phosphorylation together with V-ATPase, which contributed to cytoplasmatic pH stability; Lastly, enhancement of carbon metabolisms including TCA cycle and glycolysis accelerated the consumption of cellular organic carbon. Most of the genes in these pathways and processes showed downregulation in LAMB 122. This study disclosed the most complete transcriptional molecular mechanisms of Chlorella sp. responding to high CO 2 by combining CO 2 fixation, transportation, and metabolic processes. The results provided valuable genetic information for future screening and breeding of microalgae with high-CO 2 tolerance for more efficient CO 2 bio-sequestration. Unlabelled Image • New insights about the application of microalgae on CO 2 bio-sequestration • We provided completed molecular mechanisms of Chlorella sp. responding to high CO 2. • Upregulation genes involving carbon fixation and ATP production in LAMB 31 • Upregulation genes involving cytoplasmatic H+ transportation in LAMB 31 • Enhancement of carbon metabolisms in LAMB 31 [ABSTRACT FROM AUTHOR]

Crassostrea nippona is a commercially important oyster species in East Asia for it is edible during the summer when the other oyster species are unavailable. Salinity is one of the important limiting factors to the survival and distribution of this stenohaline species. In this study, 535 million reads (74G data) from C. nippona were produced and assembled into 66,742 transcripts. The number of 19,253 differentially expressed genes (DEGs) under salinity stress were identified as salinity stress-response genes. Through comparative evolutionary analysis in five Crassostrea species from East Asia, salinity stress-response genes were noticed to have higher adaptive evolution rates than other genes. This study presents the first de novo transcriptome of C. nippona. Furthermore, comparative evolutionary analysis implies that salinity plays an important role in speciation of Crassostrea species. [ABSTRACT FROM AUTHOR]

• The cold responsive gene expression profiles were compared in two potato genotypes. • The AGPase and INVINH expression are important for enhancing CIS resistance. • The candidate transcription factors regulating CIS resistance were identified. Potato accumulates large amounts of soluble sugar during cold storage periods. However, a system based understanding of this process is still largely unknown. Here, we compared the dynamic cold-responded transcriptome of genotypes between cold-induced sweetening resistant (CIS-R) and cold-induced sweetening sensitive (CIS-S) in tubers. Comparative transcriptome revealed that activating the pathways of starch degradation, sucrose synthesis and hydrolysis could be common strategies in response to cold in both genotypes. Moreover, the variation in sugar accumulation between genotypes may be due to genetic differences in cold response, which could be mainly explained: CIS-R genotype was active in starch synthesis and attenuated in sucrose hydrolysis by promoting the coordinate expression of a series of genes involved in starch-sugar interconversion. Additionally, transcription factors, the candidate master regulators of starch-sugar interconversion, were discussed. Taken together, this work has provided an avenue for studying the mechanism involved in the regulation of the CIS resistance. [ABSTRACT FROM AUTHOR]

• Hepatopancreatic response mechanisms of M. nipponense to sulfide stress was studied by RNA-Seq. • 235 DEGs and 123 KEGG pathways were acquired in response to sulfide stimuli. • Sulfide stress significantly altered DEGs involved in proximal tubule bicarbonate reclamation pathway. • Rap1, Sulfur metabolism, and Lysosome pathway played an important role in sulfide challenge adaptation. Aquatic environmental pollutants have various impacts on aquaculture. Specifically, sulfide has been established as being toxic to aquatic animals including the oriental river prawn Macrobrachium nipponense. In response, the hepatopancreas has been broadly studied, as it plays a pivotal role in arthropod nutrient digestion and absorption, energy supply, and organ development as well as in crustacean immunity. However, the underlying molecular mechanisms of hepatopancreas's response to sulfide toxicity are still poorly understand. Herein, we used Nova-seq 6000 platform to conduct a comparative transcriptome analysis of gene expression profiles in the hepatopancreas of M. nipponense , while it was under the influence of a semi-lethal sulfide concentration (3.20 mg/L at 48 h). A total of 139 million raw reads were obtained, in which 67,602 transcripts were clustered into 37,041 unigenes for further analysis. After constant sulfide exposure for 48 h, 235 differentially expressed genes, i.e., DEGs (151 up-regulated and 84 down-regulated) were identified in the sulfide treatment group (TGHP) compared with the control group (CGHP). We used GO and KEGG databases to annotate all the DEGs into 1180 functions and 123 pathways, respectively. The metabolic pathways included proximal tubule bicarbonate reclamation, sulfur metabolism, glycolysis and gluconeogenesis, and the TCA cycle; while immune-related pathways contained Ras, Rap1, focal adhesion and platelet activation. Additionally, apoptosis-involved pathways e.g., lysosome, also exhibited remarkable alteration in the presence of sulfide stress. Notably, responses to external stimuli and detoxification genes— such as GSKIP, CRT2, APOD, TRET1, CYP4C3 and HR39— were significantly altered by the sulfide stress, indicating that significant toxicity was transferred through energy metabolism, growth, osmoregulatory processes and immunity. Finally, we demonstrated that in the present of sulfide stress, M. nipponense altered the expression of detoxification- and extracellular stimulation-related genes, and displayed positive resistance via tight junction activation and lysosome pathways. The results of these novel experiments shed light on the hepatopancreas's molecular response to sulfide stress resistance and the corresponding adaptation mechanism; and enable us to identify several potential biomarkers for further studies. [ABSTRACT FROM AUTHOR]

• Girdling is an effective method for inducing flower formation of iron walnut. • Flower induction after girdling is mainly regulated by sugar and hormone signals. • ABA directly participated in flower induction of iron walnut. • ABA also regulated floral induction by participating in sugar regulation. Flower induction in iron walnut (Juglans sigillata) is a complex and highly regulated process involving multiple signal pathways to ensure flower bud formation in the subsequent year. However, the underlying molecular mechanism of the induction remains unknown. Girdling is an effective method for inducing flower bud formation in iron walnut. In this study, comparative transcriptome profiles between girdled (G) and ungirdled (unG) materials on the same tree were used to identify the signal pathway involved in flower bud induction by girdling in iron walnut. The results showed that genes related to starch and carbohydrate metabolism, photosynthesis, and hormone signals, including pectinesterase (PAE), trehalose 6-photosphatase (TPP), α-aminolase (α-AL), atpF , and auxin response factor ARF9 , participated in the induction process after girdling. Expression pattern of genes related to sugar metabolism revealed that sugar was the initial signal for flower induction and that photosynthesis increased after girdling, influenced by the carbon source–sink relationship. Hormone signalling networks including auxin, abscisic acid (ABA), and brassinolide also contributed to flower bud induction of iron walnut. Auxin played an important role in tissue regeneration and flower induction after girdling. ABA directly participated in flower induction. Gene expression pattern similarities between ABA and sugar metabolism signals indicated that ABA may also be involved in sugar regulation, in turn regulating floral induction. In summary, flower induction after girdling in iron walnut is mainly regulated by a polygenic network centred on sugar and hormone signals. [ABSTRACT FROM AUTHOR]

• We investigated comparative transcriptome analysis of two sweetpotato lines. • 27,636 unigenes were differentially expressed during cold storage. • These unigenes were annotated by de novo transcriptome assembly. • Many DEGs were related to carbohydrate metabolism and hormone signal transduction. Sweetpotato (Ipomoea batatas [L.] Lam) is considered an economically important crop worldwide and is used as a source of food, feed, and biomaterials. However, its origin in tropical regions makes it vulnerable to chilling injury during postharvest storage at low temperature. To gain further insight into the molecular mechanism of chilling response, we performed comparative transcriptome analysis of two sweetpotato lines, Xushu 15-1 and Xushu 15-4, with high and low cold storage ability, respectively. Tuberous roots of these lines were stored at 4 °C for 0, 2, and 6 weeks. RNA-Seq data of both lines were de novo assembled, producing 27,636 unigenes with a N50 value of 1204 bp. A total of 525 differentially expressed genes (DEGs) were identified and categorized into six clusters. Genes with higher expression in Xushu 15-1 than in Xushu 15-4 significantly increased in number over time during low temperature storage. Functional annotation of DEGs using KEGG enrichment analysis showed that these DEGs were involved in carbohydrate metabolism, ribosome, protein processing in endoplasmic reticulum, plant–pathogen interaction, and plant hormone signal transduction. Several key candidate genes involved in KEGG pathways were selected and discussed further. The results of this study enhance our understanding of the complex mechanisms involved in low temperature tolerance in sweetpotato during storage and provide a set of candidate genes for the development of new varieties with improved cold storage ability. [ABSTRACT FROM AUTHOR]

• The response mechanism of E. faecalis TV4 under fluoride exposure. • Growth inhibition effect of fluoride on E. faecalis. • Fluoride changed the energy mechanism pathway of E. faecalis. Enterococcus faecalis is one of the main components of symbiotic bacteria in the intestine of silkworm (Bombyx mori L.). The abundance of E. faecalis in the intestine of silkworm is affected by fluoride exposure. However, the response mechanism of E. faecalis toward fluoride remains largely unknown. In this study, a strain of E. faecalis (named TV4), which is a symbiotic bacteria of silkworm, was isolated and characterized. Inhibition assay showed that fluoride can significantly inhibit the growth of the TV4 strain (P < 0.05) after culture for 4 h. Finally, Illumina X-Ten platform was used to investigate the response mechanism of E. faecalis TV4 under fluoride exposure. We found that the TV4 strain demonstrated significant changes in its carbohydrate transport and metabolism and energy metabolism. The transcriptome sequencing results revealed that 237 genes were differentially expressed for TV4 grown after fluoride exposure, i.e., 92 genes were differentially up-regulated and 145 genes were differentially down-regulated. Many of the down-regulated genes were involved in cell carbohydrate transport and metabolism and energy production, whereas the up-regulated genes were mostly related to ethanolamine utilization and amino acid synthesis and metabolism. Our results revealed that strain TV4 reduced its carbohydrate metabolism and energy metabolism and increased ethanolamine utilization and amino acid metabolism to adapt and survive under fluoride exposure. This study enhances our understanding about the response mechanism of E. faecalis after fluoride exposure and has important implications for investigations on the three-way interaction among fluoride, symbiotic bacteria and silkworm. [ABSTRACT FROM AUTHOR]

• Ginkgo is rich in bioactive compounds (e.g., flavonoids and terpenoids). • 1256 differentially expressed genes were identified between young and mature leaves. • A gene in phenylpropanoid pathway was significantly upregulated. • 38 significantly different metabolites were detected between young and mature leaves. • Ginkgo metabolites promote the ginkgo-related pharmaceutical industry development. Ginkgo (Ginkgo biloba L.) is a unique medicinal tree species that mainly depends on the flavonoids and terpenoids found in its leaves. However, the biosynthesis of these metabolites is controlled and regulated by gene actions which remain poorly understood. To improve our understanding of this process, we produced a transcriptome library from young and mature leaves of ginkgo trees using the Illumina HiSeq X Ten sequencing platformin this study. We obtained a total of 57.5 million clean reads, compared with seven databases and revealed 39,404 annotated unigenes. The key differentially expressed genes (DEGs) in young and mature leaves of ginkgo were explored through GO and KEGG metabolic pathway analysis. A total of 1,256 DEGs, including 561 upregulated and 695 downregulated genes were obtained in the ginkgo transcriptome in the mature leaves compared with that of the young leaves. These genes included 23 bHLH, 9 MYB, 5 WRKY, and 4 bZIP genes that act as regulators in flavonoid and terpenoid biosynthesis. One key gene involved in the diterpenoid pathway was downregulated. A gene in the phenylpropanoid biosynthesis pathway was significantly upregulated and significantly negatively correlated with serine in metabolites. Additionally, a metabolomics analysis detected 283 metabolites, and 38 significantly different metabolites were identified. The combined metabolome and transcriptome approach employed in this study constitutes an effective method for assessing the relationships between the expression of critical genes and metabolites related to biosynthetic pathways. Our study provides new ideas for analyzing biosynthesis at the molecular level and will encourage further development of the ginkgo-related pharmaceutical industry. [ABSTRACT FROM AUTHOR]