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Abstract Background Kiwifruit, belonging to the genus Actinidia, represents a unique fruit crop characterized by its modern cultivars being genetically diverse and exhibiting remarkable variations in morphological traits and adaptability to harsh environments. However, the genetic mechanisms underlying such morphological diversity remain largely elusive. Results We report the high-quality genomes of five Actinidia species, including Actinidia longicarpa, A. macrosperma, A. polygama, A. reticulata, and A. rufa. Through comparative genomics analyses, we identified three whole genome duplication events shared by the Actinidia genus and uncovered rapidly evolving gene families implicated in the development of characteristic kiwifruit traits, including vitamin C (VC) content and fruit hairiness. A range of structural variations were identified, potentially contributing to the phenotypic diversity in kiwifruit. Notably, phylogenomic analyses revealed 76 cis-regulatory elements within the Actinidia genus, predominantly associated with stress responses, metabolic processes, and development. Among these, five motifs did not exhibit similarity to known plant motifs, suggesting the presence of possible novel cis-regulatory elements in kiwifruit. Construction of a pan-genome encompassing the nine Actinidia species facilitated the identification of gene DTZ79_23g14810 specific to species exhibiting extraordinarily high VC content. Expression of DTZ79_23g14810 is significantly correlated with the dynamics of VC concentration, and its overexpression in the transgenic roots of kiwifruit plants resulted in increased VC content. Conclusions Collectively, the genomes and pan-genome of diverse Actinidia species not only enhance our understanding of fruit development but also provide a valuable genomic resource for facilitating the genome-based breeding of kiwifruit.

Abstract HVE-400 ion implanter is special ion implantation equipment for semiconductor materials boron and phosphorus doping. The ion source and extraction deflection system are at high voltage platform, while the corresponding control system is at ground voltage position. The control signals and measurement signals of various parameters at the high-voltage end need to be transmitted between ground voltage and high voltage through optical fibers to isolate high voltage. Upgrading is carried out due to the aging of the optical fiber transmission control and monitoring system, which cannot work stably. The transformation replaces the original distributed single-point control method with an advanced distributed centralized control method, and integrates all control and monitoring functions into an industrial control computer for digital operation and display. In the computer software, two kinds of automatic calculation of ion mass number are designed. After upgrading, the implanter high-voltage platform control and monitoring system features digitalization, centralized control, high reliability, strong anti-interference, fast communication speed, and easy operation.

Citrus fruits encompass a diverse family, including oranges, mandarins, grapefruits, limes, kumquats, lemons, and others. In citrus, Agrobacterium tumefaciens–mediated genetic transformation of Hongkong kumquat (Fortunella hindsii Swingle) has been widely employed for gene function analysis. However, the perennial nature of woody plants results in the generation of transgenic fruits taking several years. Here, we show the procedures of Agrobacterium-mediated transient transformation and live-cell imaging in kumquat (F. crassifolia Swingle) fruit, using the actin filament marker GFP-Lifeact as an example. Fluorescence detection, western blot analysis, and live-cell imaging with confocal microscopy demonstrate the high transformation efficiency and an extended expression window of this system. Overall, Agrobacterium-mediated transient transformation of kumquat fruits provides a rapid and effective method for studying gene function in fruit, enabling the effective observation of diverse cellular processes in fruit biology.

Kiwifruit plants are highly susceptible to increased atmospheric temperature, and the extreme high temperature often causes the loss of production and quality of the fruit. The γ-aminobutyric acid (GABA) has been widely proved to play important roles in plants in response to abiotic stresses, showing an important potential for application in agricultural industry to overcome environmental challenges. However, application of GABA in kiwifruit plants to resist external stresses has not been reported yet. This study found that pre-irrigation of kiwifruit plants with 0.5 mM GABA was effective in alleviating the heat damage on them. GABA treatment led to better antioxidant capacity and reduced ROS production in kiwifruit plants under high temperature. Moreover, exogenous GABA protected the photosynthetic system of kiwifruit plants when exposed to high temperature. Particularly, we found that endogenous ABA, Glu, Pro metabolisms were participated in the GABA-mediated heat resistance of kiwifruit plants. Furthermore, GABA treatment induced higher expression of AdHsps in kiwifruit plants, being partly responsible for their better performance under heat stress. In summary, this research first demonstrated that exogenous GABA treatment plays a positive role in kiwifruit plants to response to extreme heat stress.

Abstract Background Light-harvesting chlorophyll a/b binding proteins (Lhcb) play crucial roles in plant growth, development, and the response to abiotic stress in higher plants. Previous studies have reported that Lhcb genes were involved in the phytochrome regulation and responded to different light and temperature conditions in Poaceae (such as maize). However, the evolution and functions of Lhcb genes remains poorly characterized in important Rosaceae species. Results In this investigation, we conducted a genome-wide analysis and identified a total of 212 Lhcb genes across nine Rosaceae species. Specifically, we found 23 Lhcb genes in Fragaria vesca, 20 in Prunus armeniaca, 33 in Malus domestica ‘Gala’, 21 in Prunus persica, 33 in Rosa chinensis, 29 in Pyrus bretschneideri, 18 in Rubus occidentalis, 20 in Prunus mume, and 15 in Prunus salicina. Phylogenetic analysis revealed that the Lhcb gene family could be classified into seven major subfamilies, with members of each subfamily sharing similar conserved motifs. And, the functions of each subfamily was predicted based on the previous reports from other species. The Lhcb proteins were highly conserved within their respective subfamilies, suggesting similar functions. Interestingly, we observed similar peaks in Ks values (0.1–0.2) for Lhcb genes in apple and pear, indicating a recent whole genome duplication event (about 30 to 45 million years ago). Additionally, a few Lhcb genes underwent tandem duplication and were located across all chromosomes of nine species of Rosaceae. Furthermore, the analysis of the cis-acting elements in the 2000 bp promoter region upstream of the pear Lhcb gene revealed four main categories: light response correlation, stress response correlation, hormone response correlation, and plant growth. Quantitative expression analysis demonstrated that Lhcb genes exhibited tissue-specific expression patterns and responded differently to low-temperature stress in Rosaceae species. Conclusions These findings shed light on the evolution and phylogeny of Lhcb genes in Rosaceae and highlight the critical role of Lhcb in pear’s response to low temperatures. The results obtained provide valuable insights for further investigations into the functions of Lhcb genes in Rosaceae, and these functional genes will be used for further fruit tree breeding and improvement to cope with the current climate changes.

Abstract Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.

ABSTRACT The tangerine pathotype of Alternaria alternata produces a host-selective toxin termed Alternaria citri toxin (ACT). The molecular mechanisms underlying the global regulation and biosynthesis of ACT remain unknown. In the present study, the function of an APSES transcription factor StuA was investigated. StuA was shown to be required for ACT biosynthesis and fungal virulence. StuA was found, for the first time, to physically interact with a pH-responsive transcription regulator PacC using yeast two-hybrid, bimolecular fluorescence complementation, and GST pull-down assays. Functional analyses revealed that StuA and PacC regulate the expression of genes involved in toxin biosynthesis and virulence. Mutation of stuA via targeted gene deletion or silencing pacC yielded fungal strains that decreased the expression of seven toxin biosynthetic genes (ACCT) and toxin production. EMSA analyses revealed that PacC could bind to the promoters of ACTT6 encoding an enoyl-CoA hydratase and ACTTR encoding an ACT pathway-specific transcription factor. Site-directed mutagenesis of five potential protein kinase A (PKA) phosphorylation sites in StuA revealed that none of the sites was involved in ACT production, indicating that the function of StuA in the regulation of ACT gene expression is not dependent on phosphorylation. Overall, our results confirmed that PacC is one of the key regulators interacting with StuA for the biosynthesis of ACT. Environmental pH may play a decisive role during A. alternata pathogenesis. Our results also revealed a previously unrecognized (StuA-PacC)→ACTTR module for the biosynthesis of ACT in A. alternata. IMPORTANCE In this study, we used Alternaria alternata as a biological model to report the role of StuA in phytopathogenic fungi. Our findings indicated that StuA is required for Alternaria citri toxin (ACT) biosynthesis and fungal virulence. In addition, StuA physically interacts with PacC. Disruption of stuA or pacC led to decreased expression of seven toxin biosynthetic genes (ACCT) and toxin production. PacC could recognize and bind to the promoter regions of ACTT6 and ACTTR. Our results revealed a previously unrecognized (StuA-PacC)→ACTTR module for the biosynthesis of ACT in A. alternata, which also provides a framework for the study of StuA in other fungi.

Torreya grandis is a gymnosperm species that produces edible seeds with high level of sciadonic acid (SCA). Here, the authors assemble the genome of this species, preform methylone analysis of seeds at different developmental stages, and reveal two key genes involved in SCA biosynthesis.

Abstract Background Chlorophyll and carotenoids, the most widely distributed lipophilic pigments in plants, contribute to fruit coloration during development and ripening. These pigments are assembled with pigment-protein complexes localized at plastid membrane. Pigment-protein complexes are essential for multiple cellular processes, however, their identity and composition in fruit have yet to be characterized. Results By using BN-PAGE technique in combination with microscopy, we studied pigment-protein complexes and plastid transformation in the purified plastids from the exocarp of citrus fruit. The discontinuous sucrose gradient centrifugation was used to isolate total plastids from kumquat fruit, and the purity of isolated plastids was assessed by microscopy observation and western blot analysis. The isolated plastids at different coloring stages were subjected to pigment autofluorescence observation, western blot, two-dimensional electrophoresis analysis and BN-PAGE assessment. Our results demonstrated that (i) chloroplasts differentiate into chromoplasts during fruit coloring, and this differentiation is accompanied with a decrease in the chlorophyll/carotenoid ratio; (ii) BN-PAGE analysis reveals the profiles of macromolecular protein complexes among different types of plastids in citrus fruit; and (iii) the degradation rate of chlorophyll-protein complexes varies during the transition from chloroplasts to chromoplasts, with the stability generally following the order of LHCII > PS II core > LHC I > PS I core. Conclusions Our optimized methods for both plastid separation and BN-PAGE assessment provide an opportunity for developing a better understanding of pigment-protein complexes and plastid transitions in plant fruit. These attempts also have the potential for expanding our knowledge on the sub-cellular level synchronism of protein changes and pigment metabolism during the transition from chloroplasts to chromoplasts.

The number of studies on plant transcriptomes using ONT RNAseq technology is rapidly increasing in recent. It is a powerful method to decipher transcriptomic complexity, particularly alternative splicing (AS) event detection. Citrus plants are the most important widely grown fruit crops. Exploring different AS events in citrus contributes to transcriptome improvement and functional genome study. Here, we performed ONT RNAseq in 9 species (Atalantia buxifolia, Citrus clementina, C. grandis, C. ichangensis, C. reticulata, C. sinensis, Clausena lansium, Fortunella hindsii, and Poncirus trifoliata), accompanied with Illumina sequencing. Non-redundant full-length isoforms were identified between 41,957 and 76,974 per species. Systematic analysis including different types of isoforms, number of isoforms per gene locus, isoform distribution, ORFs and lncRNA prediction and functional annotation were performed mainly focused on novel isoforms, unraveling the capability of novel isoforms detection and characterization. For AS events prediction, A3, RI, and AF were overwhelming types across 9 species. We analyzed isoform similarity and evolutionary relationships in all species. We identified that multiple isoforms derived from orthologous single copy genes among different species were annotated as enzymes, nuclear-related proteins or receptors. Isoforms with extending sequences on 5’, 3’, or both compared with reference genome were filtered out to provide information for transcriptome improvement. Our results provide novel insight into comprehending complex transcriptomes in citrus and valuable information for further investigation on the function of genes with diverse isoforms.

Spinach is a nutritious leafy vegetable growing worldwide. Here, the authors report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 accessions, and provide insights into spinach domestication and the genetic basis of agronomic traits.

Waterlogging stress has an enormous negative impact on the kiwifruit yield and quality. The protective role of exogenous melatonin on water stress has been widely studied, especially in drought stress. However, the research on melatonin-induced waterlogging tolerance is scarce. Here, we found that treatment with exogenous melatonin could effectively alleviate the damage on kiwifruit plants in response to waterlogging treatment. This was accompanied by higher antioxidant activity and lower ROS accumulation in kiwifruit roots during stress period. The detection of changes in amino acid levels of kiwifruit roots during waterlogging stress showed a possible interaction between melatonin and amino acid metabolism, which promoted the tolerance of kiwifruit plants to waterlogging. The higher levels of GABA and Pro in the roots of melatonin-treated kiwifruit plants partly contributed to their improved waterlogging tolerance. In addition, some plant hormones were also involved in the melatonin-mediated waterlogging tolerance, such as the enhancement of ACC accumulation. This study discussed the melatonin-mediated water stress tolerance of plants from the perspective of amino acid metabolism for the first time.

Highly efficient genetic transformation technology is greatly beneficial for crop gene function analysis and precision breeding. However, the most commonly used genetic transformation technology for woody plants, mediated by Agrobacterium tumefaciens, is time-consuming and inefficient, which limits its utility for gene function analysis. In this study, a simple, universal, and highly efficient genetic transformation technology mediated by A. rhizogenes K599 is described. This technology can be applied to multiple citrus genotypes, and only 2–8 weeks were required for the entire workflow. Genome-editing experiments were simultaneously conducted using 11 plasmids targeting different genomic positions and all corresponding transformants with the target knocked out were obtained, indicating that A. rhizogenes-mediated genome editing was highly efficient. In addition, the technology is advantageous for investigation of specific genes (such as ACD2) for obtaining “hard-to-get” transgenic root tissue. Furthermore, A. rhizogenes can be used for direct viral vector inoculation on citrus bypassing the requirement for virion enrichment in tobacco, which facilitates virus-induced gene silencing and virus-mediated gene expression. In summary, we established a highly efficient genetic transformation technology bypassing tissue culture in citrus that can be used for genome editing, gene overexpression, and virus-mediated gene function analysis. We anticipate that by reducing the cost, required workload, experimental period, and other technical obstacles, this genetic transformation technology will be a valuable tool for routine investigation of endogenous and exogenous genes in citrus.

Alternaria brown spot (ABS), caused by Alternaria alternata, is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford Nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N50 of 3.08 Mb. The genome is encompassed 12,067 protein-coding genes, 34 ribosomal RNAs, and 107 transfer RNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes and 2 CDCs, which is consistent with the experimental evidences of pulsed-field gel electrophoresis. To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria spp. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria spp. are available. The citrus-related Alternaria genomes database is open accessible through the Citrus Fungal Disease Database.[Graphic: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

In order to draw a high-quality single-bounce capillary (SBC) to meet various applications, there is an increasing demand for detailed simulations of the SBC. In this study, a code based on the ray-tracing method was developed to simulate SBCs in detail for various X-ray sources to optimize their performances by considering factors such as attenuation of X-rays, coating, X-ray source characteristics (spot-size, distribution of energy, and intensity), surface shape errors, centerline errors, surface roughness, and absorption edges of X-rays. This code has monochrome and polychrome modes which were usually used to simulate the monoenergetic and polyenergetic performances of the SBC.

Histone methylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs). This study determined the function of 5 HMTs (AaDot1, AaHMT1, AaHnrnp, AaSet1, and AaSet2) and 1 HDMs (AaGhd2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. The vegetative growth, conidiation, and pathogenicity of ∆AaSet1 and ∆AaSet2 were severely inhibited indicating that AaSet1 and AaSet2 play critical roles in cell development in A. alternata. Multiple stresses analysis revealed that both AaSet1 and AaSet2 were involved in the adaptation to cell wall interference agents and osmotic stress. Meanwhile, ∆AaSet1 and ∆AaSet2 displayed serious vegetative growth defects in sole carbon source medium, indicating that AaSet1 and AaSet2 play an important role in carbon source utilization. In addition, ∆AaSet2 colony displayed white in color, while the wild-type colony was dark brown, indicating AaSet2 is an essential gene for melanin biosynthesis in A. alternata. AaSet2 was required for the resistance to oxidative stress. On the other hand, all of ∆AaDot1, ∆AaHMT1, and ∆AaGhd2 mutants displayed wild-type phenotype in vegetative growth, multi-stress resistance, pathogenicity, carbon source utilization, and melanin biosynthesis. To explore the regulatory mechanism of AaSet1 and AaSet2, RNA-seq of these mutants and wild-type strain was performed. Phenotypes mentioned above correlated well with the differentially expressed genes in ∆AaSet1 and ∆AaSet2 according to the KEGG and GO enrichment results. Overall, our study provides genetic evidence that defines the central role of HMTs and HDMs in the pathological and biological functions of A. alternata.

Monocapillary x-ray lenses (MXRLs) are mostly used as condensers in full-field transmission x-ray microscopy (TXM) based on synchrotron radiation or laboratory x-ray tubes. The performance of the condenser has a significant impact on the imaging quality of the TXM. In this paper, a procedure for the characterization of the MXRL as a condenser is presented. The procedure mainly includes two parts: optical measurement and x-ray tests. From the test results of the characterization procedure, it can be seen that a relatively high-performance condenser can be screened out from a series of MXRLs drawn by an electric furnace. This is also fed back to the manufacturing process, and therefore, the technology of manufacturing the condenser can be gradually optimized. Moreover, the method of characterizing the performance of the condenser designed for synchrotron radiation TXM by laboratory x-ray tubes is proposed to be used in this procedure, which effectively reduces the manufacturing time of high-performance condensers for synchrotron radiation TXM.

Autophagy is a conserved degradation pathway in plants, which plays an important role in plant cellular homeostasis during abiotic stress. Although various abiotic stressors have been reported to induce autophagic activity in plants, the specific role of autophagy in plant cadmium (Cd) tolerance remains undiscovered. In this study, we treated three MdATG10-overexpressing apple lines with hydroponic Cd stress and found the enhanced Cd tolerance in transgenic plants. Transgenic apple plants exhibited less growth limitation and reduced Cd damage on the photosynthetic system. That was accompanied by higher antioxidant enzymes activity and lower harmful ROS accumulation in apple leaves under Cd stress. The higher autophagic activity led to a more active metabolic system of Pro, His, and Arg in transgenic plants under Cd stress, which was closely related to the plant Cd tolerance. In addition, the transcriptional activities of several Cd transport and detoxification-related genes were regulated by MdATG10-overexpression in response to Cd stress. This study is the first to demonstrate the protective role of autophagy in the Cd tolerance of plants.

Host-pathogen interactions are the result of the continuously evolving dynamics of the genomic interphases between pathogens and the host plants. Alternaria brown spot (ABS) caused by the pathogen Alternaria alternata is a serious threat to tangerine production. Although recent studies have made significant advances in the characterization of A. alternata virulence factors, a gap exists in the regulation of virulent genes throughout the course of A. alternata infection on host plants. To gain a better understanding of the dynamic defense transcriptome in Alternaria alternata during Infection, we performed a comparative transcriptome approach. After inoculation on citrus, we found that 2142, 1964, 2359 genes were up-regulated, and 1948, 1434, 1996 genes were down-regulated at 12 hours-post-inoculation (hpi), 24 hpi and 48 hpi, respectively. Among these genes, 1333 genes were up-regulated at three time points, and 1054 genes were down-regulated, indicating that most of the differentially expressed genes at the early stage of infection tended to remain differentially expressed at the later stage of infection. In addition to the genes that are known to be part of the infection network in plant-pathogen interactions, many novel genes related to plant-pathogen interaction were identified. Interestingly, our results indicate that A. alternata is able to rapidly alter its gene expression pattern during infection process, which is vital for the successful colonization of the pathogen. Moreover, this rapid alteration of gene expression is likely to be an adaptive mechanism, enabling the pathogen to quickly respond to any changes in the environment and adapt to the host’s defense system. This ability to modify gene expression quickly in the face of environmental changes could play a critical role in the successful establishment of infection. RT-qPCR analysis confirmed that the expression pattern of nine randomly selected genes from the peroxisome pathway were consistent with the RNA-seq data. Our study provided a comprehensive study of the expression of genes during A. alternata infection of citrus, which may facilitate the understanding of host-plant interactions in A. alternata.

Alternaria brown spot disease is caused by the Alternaria alternata tangerine pathotype, which relies on ACT-toxin for infection. At present, all identified ACT-toxin biosynthesis-related genes are multi-copy genes. In this study, we summarized the advances in important host-specific toxins (HSTs), and listed key genes required for the pathogenicity of the A. alternata tangerine pathotype. Toxin virulence test results revealed that different citrus species displayed distinctly different tolerances to ACT-toxin. The extraction method of ACT-toxin crude extract was described in schematic form to make the method easier to understand. In addition, target gene disruption of two copies of ACTT5 (∆∆ACTT5) displayed significantly reduced virulence, indicating that ACTT5 is essential for the pathogenicity of the A. alternata tangerine pathotype.

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The molecular mechanisms behind the interactions between bacteria and fungi are largely unclear. Here, Chen et al. show that a compound secreted by bacteria from the wheat head microbiome inhibits growth and virulence of a plant pathogenic fungus by manipulating fungal histone modification.

Spinach is an economically important vegetable crop but previous genomic resources were of limited use for comparative and functional analyses. Here, Xuet al. present a high quality draft spinach genome and transcriptome data for multiple Spinaciaaccessions providing insight into Caryophyllales genome evolution.

The necrotrophic fungal pathogen Alternaria alternata attacks many citrus species, causing brown spot disease. Its pathogenic capability depends primarily on the production of host-selective ACT toxin. In the current study a Ste12 transcription factor was characterized to be required for conidial formation and the production of cell-wall-degrading enzymes (CWDEs) in the tangerine pathotype of A. alternata. The Ste12 deficiency strain (ΔSte12) retained wild-type growth, ACT toxin production, and sensitivity to oxidative and osmotic stress. However, pathogenicity tests assayed on detached Dancy leaves revealed a marked reduction in virulence of ΔSte12. Transcriptome and quantitative RT-PCR analyses revealed that many genes associated with Carbohydrate-Active Enzymes (CAZymes) were downregulated in ΔSte12. Two cutinase-coding genes (AaCut3 and AaCut7) regulated by Ste12 were individually and simultaneously inactivated. The AaCut3 or AaCut7 deficiency strain unchanged in cutinase activities and incited wild-type lesions on Dancy leaves. However, the strain carrying an AaCut3 AaCut7 double mutation produced and secreted significantly fewer cutinases and incited smaller necrotic lesions than wild type. Not only is the host-selective toxin (HST) produced by A. alternata required for fungal penetration and lesion formation, but so too are CWDEs required for full virulence. Overall, this study expands our understanding of how A. alternata overcomes citrus physical barriers to carry out successful penetration and colonization.

The sterol regulatory element binding proteins (SREBPs) are key regulators for sterol homeostasis in most fungi. In the citrus postharvest pathogen Penicillium digitatum, the SREBP homolog is required for fungicide resistance and regulation of CYP51 expression. In this study, we identified another SREBP transcription factor PdSreB in P. digitatum, and the biological functions of both SREBPs were characterized and compared. Inactivation of PdsreA, PdsreB or both genes in P. digitatum reduced ergosterol contents and increased sensitivities to sterol 14-α-demethylation inhibitors (DMIs) and cobalt chloride. Fungal strains impaired at PdsreA but not PdsreB increased sensitivity to tridemorph and an iron chelator 2,2'-dipyridyl. Virulence assays on citrus fruit revealed that fungal strains impaired at PdsreA, PdsreB or both induce maceration lesions similar to those induced by wild-type. However, ΔPdsreA, ΔPdsreB or the double mutant strain rarely produce aerial mycelia on infected citrus fruit peels. RNA-Seq analysis showed the broad regulatory functions of both SREBPs in biosynthesis, transmembrane transportation and stress responses. Our results provide new insights into the conserved and differentiated regulatory functions of SREBP homologs in plant pathogenic fungi.

Evolution of gene regulation has been proposed to play an important role in environmental adaptation. Exploring mechanisms underlying coordinated evolutionary changes at various levels of gene regulation could shed new light on how organism adapt in nature. In this study, we focused on regulatory differences between a laboratory Saccharomyces cerevisiae strain BY4742 and a pathogenic S. cerevisiae strain, YJM789. The two strains diverge in many features, including growth rate, morphology, high temperature tolerance, and pathogenicity. Our RNA-Seq and ribosomal footprint profiling data showed that gene expression differences are pervasive, and genes functioning in mitochondria are mostly divergent between the two strains at both transcriptional and translational levels. Combining functional genomics data from other yeast strains, we further demonstrated that significant divergence of expression for genes functioning in the electron transport chain (ETC) was likely caused by differential expression of a transcriptional factor, HAP4, and that post-transcriptional regulation mediated by an RNA-binding protein, PUF3, likely led to expression divergence for genes involved in mitochondrial translation. We also explored mito-nuclear interactions via mitochondrial DNA replacement between strains. Although the two mitochondrial genomes harbor substantial sequence divergence, neither growth nor gene expression were affected by mitochondrial DNA replacement in both fermentative and respiratory growth media, indicating compatible mitochondrial and nuclear genomes between these two strains in the tested conditions. Collectively, we used mitochondrial functions as an example to demonstrate for the first time that evolution at both transcriptional and post-transcriptional levels could lead to coordinated regulatory changes underlying strain specific functional variations.

N6-methyladenosine (m6A) RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms. Despite its significance, a comprehensive analysis of m6A-related genes in non-model plants, such as kiwifruit, is lacking. Here, we identified 36 m6Arelated genes in the kiwifruit genome according to homology and phylogenetic inference. We performed bioinformatics and evolutionary analyses of the writer, eraser, and reader families of m6A modification. Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most m6A-related genes were remarkably expressed under different conditions. Through construction of gene co-expression networks, we found significant correlations between several m6A-related genes and transcription factors (TFs) as well as receptor-like genes during the development and ripening of kiwifruit. Furthermore, we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of m6A-related genes. We identified 10 common open chromatin regions that were present in at least two tissues, and these regions might serve as potential binding sites for MADS protein, C2H2 protein, and other predicted TFs. Our study offers comprehensive insights into the gene family of m6A-related components in kiwifruit, which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit. [ABSTRACT FROM AUTHOR]