Plant-pathogen Interaction Pathway Research Articles

Complete genome sequence of the Pogostemon cablin bacterial wilt pathogen Ralstonia solanacearum strain SY1.

BackgroundRalstonia solanacearum causes bacterial wilt of Pogostemon cablin which is an important aromatic herb and also the main materials of COVID-19 therapeutic traditional drugs. However, we are lacking the information on the genomic sequences of R. solanacearum isolated from P. cablin.ObjectiveThe acquisition and analysis of this whole-genome sequence of the P. cablin bacterial wilt pathogen.MethodsAn R. solanacearum strain, named SY1, was isolated from infected P. cablin plants, and the complete genome sequence was sequenced and analyzed.ResultsThe SY1 strain contains a 3.70-Mb chromosome and a 2.18-Mb megaplasmid, with GC contents of 67.57% and 67.41%, respectively. A total of 3308 predicted genes were located on the chromosome and 1657 genes were located in the megaplasmid. SY1 strain has 273 unique genes compared with five representative R. solanacearum strains, and these genes were enriched in the plant–pathogen interaction pathway. SY1 possessed a higher syntenic relationship with phylotype I strains, and the arsenal of type III effectors predicted in SY1 were also more closely related to those of phylotype I strains. SY1 contained 14 and 5 genomic islands in its chromosome and megaplasmid, respectively, and two prophage sequences in its chromosome. In addition, 215 and 130 genes were annotated as carbohydrate-active enzymes and antibiotic resistance genes, respectively.ConclusionThis is the first genome-scale assembly and annotation for R. solanacearum which isolated from infected P. cablin plants. The arsenal of virulence and antibiotic resistance may as the determinants in SY1 for infection of P. cablin plants.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13258-022-01270-9.

Transcriptomic differences in response to Metarhizium anisopliae and Trichoderma harzianum uncovers major regulative genes and pathways for establishment of beneficial relationship in peanut

The fungi Metarhizium anisopliae and Trichoderma harzianum are important biocontrol agents and play a pivotal role in insect pests and plant pathogens control. They can also promote plant growth and survival in plants as endophytes. However, the endogenous mechanism is still unclear and needs further studies. Here in the current study, we analyzed the transcriptomic changes in the response of peanut roots inoculated with the two fungi for 4 days. The two transcriptomic data revealed 119 and 856 differentially expressed genes (DEGs) which were respectively induced by M. anisopliae and T. harzianum in inoculated peanut roots. KEGG library showed the DEGs from M. anisopliae treatment were scattered in diverse pathways, whereas the DEGs from T. harzianum treatment were top enriched in phenylpropanoid biosynthesis and plant-pathogen interaction pathways. Furthermore, there were 76 shared DEGs under the induction of two fungi, which were highly enriched in stress-resistant pathways including hormone signal transduction, linolenic acid metabolism, and phenylpropanoid biosynthesis. Independently, 43 DEGs were specifically induced by M. anisopliae which is mainly involved in plant defense, stress-resistant response and cell nutrition, whereas 780 DEGs were specifically induced by T. harzianum which were top enriched in plant-pathogen interaction, hormone signal transduction and phenylpropanoid biosynthesis. 11 genes in mentioned pathways were selected for RT-qPCR analysis which was almost consistent with transcriptomic data. Findings suggested that both M. anisopliae and T. harzianum can up-regulate the transcription levels of abscisic acid receptors, ethylene transcription factors, and linolenic acid metabolism genes to regulate hormone signal transduction pathways and linolenic acid metabolism pathways for successful penetration or colonization. Differently, T. harzianum mainly strengthened the inhibition of the plant immune response and induction of plant system disease resistance, while M. anisopliae slightly weakened the immune response but multi-regulated pathways for nutritional transport and metabolism, especially in nitrogen and iron ion supply for symbiotic initiation.

Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response.

Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant–pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein–protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN–soybean interaction mechanism as a model will present more understanding of other plant–nematode interactions.

Transcript profiling of papaya (Carica papaya L.) with CTS-N fertiliser after inoculation with PRSV

ABSTRACT CTS-N is deacetylation chitosan that can induce the expression of defence genes in plants. PRSV is a virus that can infect papaya and cause disease. It is mainly distributed in tropical and subtropical regions all over the world. The epidemic spread of the virus may seriously affect the papaya industry. In this study, we analysed differently expressed genes that are related to disease resistance after applying CTS-N using RNA-seq and subsequent qPCR analysis. Several genes related to plant defence responses, such as PR-1 and WRKY33, were up-regulated. Among the genes, 10 up-regulated and 2 down-regulated genes were involved in the ‘plant pathogen interaction pathway’, ‘phytohormones signal transduction pathway’ and ‘amino sugars pathway’. The CTS-N treatment(1.0 ml/L) can significantly prevent the damage to papaya plants caused by PRSV. The RNA profiling results indicated that CTS-N can induce the expression of defence related genes to enhances a degree of plant defence. Future research may include comparable methodologies for disease resistance research in other plant species.

Functional Annotation of circRNAs in Tea Leaves After Infection by the Tea Leaf Spot Pathogen, Lasiodiplodia theobromae.

Tea leaf spot, caused by Lasiodiplodia theobromae, is an important disease that can seriously decrease the production and quality of tea (Camellia sinensis (L.) O. Kuntze) leaves. The analysis of circular RNA (circRNA) in tea leaves after infection by the pathogen could improve understanding about the mechanism of host-pathogen interactions. In this study, high-performance sequencing of circRNA from C. sinensis Fuding-dabaicha leaves that had been infected with L. theobromae was conducted using the Illumina HiSeq 4000 platform. In total, 192 and 153 differentially expressed circRNAs from tea leaves were significantly up- and downregulated, respectively, after infection with L. theobromae. A gene ontology analysis indicated that the differentially expressed circRNA-hosting genes for DNA binding were significantly enriched. The genes with significantly differential expressions that were annotated in the specified database (S genes) were σ factor E isoform 1, triacylglycerol lipase SDP1, DNA-directed RNA polymerase III subunit 2, WRKY transcription factor WRKY24, and regulator of nonsense transcripts 1 homolog. A Kyoto Encyclopedia of Genes and Genomes analysis indicated that the significantly enriched circRNA-hosting genes involved in the plant-pathogen interaction pathway were Calmodulin-domain protein kinase 5 isoform 1, probable WRKY transcription factor 33, U-box domain-containing protein 35, probable inactive receptor-like protein kinase At3g56050, WRKY transcription factor WRKY24, mitogen-activated protein kinase kinase kinase YODA, SGT1, and protein DGS1. Functional annotation of circRNAs in tea leaves infected by L. theobromae will provide a valuable resource for future research on host-pathogen interactions.

Comparative physiological and transcriptomic profiles reveal regulatory mechanisms of soft rot disease resistance in Amorphophallus spp.

Amorphophallus spp. are important industrial crops in Southwest China. Unfortunately, bacterial disease is one of the factors limiting the development of the Amorphophallus spp. industry. Soft rot can be caused by the pathogen Pectobacterium carotovorum subsp. carotovorum (Pcc) and leads to large-scale losses in Amorphophallus spp. quality and production. However, the mechanisms underlying the response of Amorphophallus spp. to Pcc remain largely unknown. This study compared two species of Amorphophallus, A. muelleri and A. konjac, to explore Pcc resistance by combined physiological and transcriptome analysis. On the basis of phenotype analysis, A. muelleri exhibited higher resistance to Pcc than A. konjac. Moreover, the transcriptomes of A. muelleri and A. konjac were assembled, and differentially expressed genes (DEGs) were annotated. Significant categories including the plant hormone transduction pathway, phenylpropanoid biosynthesis pathway and plant pathogen interaction pathway were identified. Among these pathways, small auxin upregulated RNA (SAUR), ethylene responsive transcription factor 1 (ERF1), 4-coumarate-CoA ligase (4CL), peroxidase (POD), WRKY transcription factor, Ca2+ sensor-related and mitogen-activated protein kinase (MAPK) genes were upregulated in A. muelleri, which may be involved in the regulation of energy, oxidative stress and signal transduction upon exposure to Pcc infection. The transcription levels of four selected genes were further verified by quantitative real-time PCR. Overall, this study identifies several critical genes involved in resistance to soft rot disease in Amorphophallus spp. and provides a theoretical foundation for identifying potential targets for metabolic engineering for disease control.

Combined Transcriptome and Metabolome Analysis of Musa nana Laur. Peel Treated With UV-C Reveals the Involvement of Key Metabolic Pathways.

An increasing attention is being given to treat fruits with ultraviolet C (UV-C) irradiation to extend shelf-life, senescence, and protection from different diseases during storage. However, the detailed understanding of the pathways and key changes in gene expression and metabolite accumulation related to UV-C treatments are yet to be explored. This study is a first attempt to understand such changes in banana peel irradiated with UV-C. We treated Musa nana Laur. with 0.02 KJ/m2 UV-C irradiation for 0, 4, 8, 12, 15, and 18 days and studied the physiological and quality indicators. We found that UV-C treatment reduces weight loss and decay rate, while increased the accumulation of total phenols and flavonoids. Similarly, our results demonstrated that UV-C treatment increases the activity of defense and antioxidant system related enzymes. We observed that UV-C treatment for 8 days is beneficial for M. nana peels. The peels of M. nana treated with UV-C for 8 days were then subjected to combined transcriptome and metabolome analysis. In total, there were 425 and 38 differentially expressed genes and accumulated metabolites, respectively. We found that UV-C treatment increased the expression of genes in secondary metabolite biosynthesis related pathways. Concomitant changes in the metabolite accumulation were observed. Key pathways that were responsive to UV-C irradiation include flavonoid biosynthesis, phenylpropanoid bios6ynthesis, plant-pathogen interaction, MAPK signaling (plant), and plant hormone signal transduction pathway. We concluded that UV-C treatment imparts beneficial effects on banana peels by triggering defense responses against disease, inducing expression of flavonoid and alkaloid biosynthesis genes, and activating phytohormone and MAPK signaling pathways.

Functional Annotation of circRNAs of Tea Leaves During Infection by the Tea Leaf Spot Pathogen Didymella segeticola

Didymella segeticola (Q. Chen) Q. Chen, Crous & L. Cai (syn. Phoma segeticola) is an important phytopathogen that causes leaf spot on tea, Camellia sinensis [L.] O. Kuntze, which results in huge tea production losses. The functional annotation and analysis of circular RNAs (circRNAs) of tea leaves during D. segeticola infection may reveal the host–pathogen interaction mechanisms. In this study, a model of tea (C. sinensis ‘Fuding-dabaicha’) leaves infected by D. segeticola was constructed, and then circRNAs of tea leaves were sequenced on the Illumina HiSeq 4000 platform. In total, 231 and 118 differentially expressed circRNAs from tea leaves were significantly up- and down-regulated, respectively, by the D. segeticola infection. A Kyoto Encyclopedia of Genes and Genomes analysis indicated that the differentially expressed circRNA-hosting-genes were significantly enriched in the plant–pathogen interaction pathway. As the differentially expressed circRNA-hosting-gene of circRNA in the pathway, the U-box domain-containing protein 35 gene was enriched in response to stress according to a Gene Ontology analysis. The expression profiling of circRNAs and the annotation of circRNA-hosting-genes of tea leaves during D. segeticola infection will provide a resource for future research on host–pathogen interactions.

Identification and Fine Mapping of the Recessive Gene BK-5, Which Affects Cell Wall Biosynthesis and Plant Brittleness in Maize.

The cellulose of the plant cell wall indirectly affects the cell shape and straw stiffness of the plant. Here, the novel brittleness mutant brittle stalk-5 (bk-5) of the maize inbred line RP125 was characterized. We found that the mutant displayed brittleness of the stalk and even the whole plant, and that the brittleness phenotype existed during the whole growth period from germination to senescence. The compressive strength was reduced, the cell wall was thinner, and the cellulose content was decreased compared to that of the wild type. Genetic analysis and map-based cloning indicated that bk-5 was controlled by a single recessive nuclear gene and that it was located in a 90.2-Kb region on chromosome 3 that covers three open reading frames (ORFs). Sequence analysis revealed a single non-synonymous missense mutation, T-to-A, in the last exon of Zm00001d043477 (B73: version 4, named BK-5) that caused the 951th amino acid to go from leucine to histidine. BK-5 encodes a cellulose synthase catalytic subunit (CesA), which is involved with cellulose synthesis. We found that BK-5 was constitutively expressed in all tissues of the germinating stage and silking stage, and highly expressed in the leaf, auricula, and root of the silking stage and the 2-cm root and bud of the germinating stage. We found that BK-5 mainly localized to the Golgi apparatus, suggesting that the protein might move to the plasma membrane with the aid of Golgi in maize. According to RNA-seq data, bk-5 had more downregulated genes than upregulated genes, and many of the downregulated genes were enzymes and transcription factors related to cellulose, hemicellulose, and lignin biosynthesis of the secondary cell wall. The other differentially expressed genes were related to metabolic and cellular processes, and were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and the plant–pathogen interaction pathway. Taken together, we propose that the mutation of gene BK-5 causes the brittle stalk phenotype and provides important insights into the regulatory mechanism of cellulose biosynthesis and cell wall development in maize.

Glutamine synthetase gene PpGS1.1 negatively regulates the powdery mildew resistance in Kentucky bluegrass.

Excessive nitrogen (N) application may induce powdery mildew (PM) in perennial grasses, but the resistance mechanisms to PM remain unclear. This study evaluated the physiological and molecular mechanisms of PM resistance affected by N supplies in Kentucky bluegrass (Poa pratensis L.). Cultivar 'Bluemoon' (N tolerant) and 'Balin' (N sensitive) were treated with low N (0.5mM), normal N (15mM), and high N (30mM) for 21d in a greenhouse. With increasing N levels, the disease growth was more severe in 'Balin' than in 'Bluemoon'. RNA-seq and weighted gene coexpression network analysis revealed that the PpGS1.1 gene encoding glutamine synthetase was a potential hub gene for PM resistance after comparisons across cultivars and N treatments. The N metabolism pathway was connected with the plant-pathogen interaction pathway via PpGS1.1. The expression of PpGS1.1 in rice protoplasts indicated that the protein was located in the nucleus and cytoplasm. Overexpression of PpGS1.1 in wild-type Kentucky bluegrass increased carbon and N contents, and the transgenic plants became more susceptible to PM with a lower wax density. The most differentially expressed genes (DEGs) for N metabolism were upregulated and DEGs for fatty acid metabolism pathway were downregulated in the overexpression lines. The results elucidated mechanisms of PM resistance in relation to N metabolism in Kentucky bluegrass.

Gene mining to discover pumpkin response genes to gummy stem blight infection caused by Stagonosporopsis cucurbitacearum

ABSTRACT Pumpkin is one of the region’s main cashcrops in northeast China cultivated for its edible seed and sarcocarp. Gummy stem blight (GSB), caused by the main pathogenic fungus of Stagonosporopsis cucurbitacearum (Sc.) which was identified in our previous study, has hampered pumpkin industry development with the affection of its reduced biological yield and edible quality. To clear the plant immune response mechanisms against Sc. infection, RNA-seq technology was employed to sequence pumpkin leaf transcriptome, the total number of distinct differentially expressed genes (DEGs) between the treatments and control was 2351, 4892, 5285, 4698, and 4213 for 2, 6, 12, 24, and 96 h treatments, respectively. KEGG analysis results revealed 16 distinct significantly up-regulated DEGs associated with MAPK signaling and plant-pathogen interaction pathways that may actively participate in Sc. infection-associated processes, while other five DEGs exhibited significantly altered expression during GSB infection. An apyrase-like gene, Gene3360 (LOC111476496), with significantly different expression levels, was possessing an early-stage primary infection-based function, which was hypothesized an important role in the resistance of pumpkin to Sc. infection. This study further deepens our understanding of the mechanism and mechanism of pumpkin leaf resistance to fungal infection.

RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors for Hevea brasiliensis Reaction Wood Formation.

Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF–gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.

Transciptome Analysis Molecular Mechanism of Starch Synthesis During Tuber Development in Chinese Yam (Dioscorea opposita)

Yam (Dioscorea opposita) is a kind of vegetables with important nutritional, medicinal and economic value. To reveal the relationship between starch synthesis and gene expression in yam tubers at gene transcription level, transcriptome profiling was conducted by RNA-Seq in Bikeqi yam (Dioscorea opposita Thunb.) tubers at five key developmental stages (105, 120, 135, 150, and 165 days after sowing, DAS). Based on transcriptome sequencing data, a total of 45,867 unigenes were obtained. The results showed that 135 days after sowing are the key period of starch accumulation. During yam tuber development, 1,941 candidate differentially expressed genes (DEGs) were successfully classified into three GO categories, respectively, and there were 292, 267 and 478 unigenes in cellular component, molecular function and biological process. There were 767, 90 and 73 DEGs enriched in metabolic, plant hormone signal transduction and Plant-pathogen interaction pathway by Kyoto Encyclopedia of Genes and Genomes (KEGG), individually. Especially 72 DEGs were enriched in starch and sucrose metabolism pathway. In this pathway, the metabolic process was mainly positive regulated by genes encoding sucrose synthase, glucose-1-phosphate adenylyltransferase, alpha-trehalase, and so on. There was negative regulated by genes encoding beta-glucosidase. 10 DEGs involved in starch synthesis were selected to prove the accuracy of the RNA-Seq data by qPCR, 85% (34/40) of the results were consistent. The results lay a theoretical foundation be used for further understanding the starch synthesis mechanism of yam tubers development and accelerating breeding progress.

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.).

The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae.

Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.

Genome-Wide Characterization of HSP90 Gene Family in Malus sieversii and Their Potential Roles in Response to Valsa mali Infection

Heat shock protein 90 (HSP90) is highly conservative molecular chaperon produced by plants in response to adverse environmental stresses including fungal infection. In China, canker disease, caused by Valsa mali, is the main threat for Malus sieversii, an ancestor of the cultivated apple. In this study, a total of eight HSP90 genes were identified from the M. sieversii genome and randomly distributed on eight chromosomes. According to gene structure and phylogenetic analysis, the MsHSP90s can be divided into five categories. The transcriptome analysis of M. sieversii under V. mali infection showed that the plant pathogen interaction pathway was identified as significantly enriched. RNA-seq data and qRT-PCR analysis demonstrated that the MsHSP90-6a gene was significantly repressed by V. mali infection. We further predicted cis-regulatory elements on the promotor region of MsHSP90 genes and identified canonical SHE motifs. Our results improve our understanding of the HSP90 gene family and provide a foundation for further studies of disease prevention in M. sieversii.

Identification of Potential Gene Regulatory Pathways Affecting the Ratio of Four-Seed Pod in Soybean.

The number of four-seed pods is one of the most important agronomic traits affected by gene and environment that can potentially improve soybean (Glycine max) yield. However, the gene regulatory network that affects the ratio of four-seed pod (the ratio of the number of four-seed pods to the total number of pods in each individual plant) is yet unclear. Here, we performed bulked segregant RNA sequencing (BSR-seq) on a series of recombinant inbred lines (RILs) derived from hybrid progenies between Heinong 48 (HN48), a cultivar with a high ratio of four-seed pod, and Henong 64 (HN64), a cultivar with a low ratio of four-seed pod. Two tissues, flower bud and young pod, at two different growth stages, R1 and R3, were analyzed under the ratios of four-seed pod at less than 10% and greater than 30%, respectively. To identify the potential gene regulation pathways associated with the ratio of soybean four-seed pod, we performed differentially expressed analysis on the four bulked groups. A differentially expressed gene (DEG) encoding a photosystem II 5-kDa protein had the function of participating in the energy conversion of photosynthesis. In addition, 79 common DEGs were identified at different developmental stages and under different ratios of four-seed pod. Among them, four genes encoding calcium-binding proteins and a WRKY transcription factor were enriched in the plant–pathogen interaction pathway, and they showed a high level of expression in roots. Moreover, 10 DEGs were identified in the reported quantitative trait locus (QTL) interval of four-seed pod, and two of them were significantly enriched in the pentose and glucuronate interconversion pathway. These findings provide basic insights into the understanding of the underlying gene regulatory network affected by specific environment and lay the foundation for identifying the targets that affect the ratio of four-seed pod in soybean.

The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and DgWRKYs may cooperate in the immunity against rust.

Orchardgrass (Dactylis glomerata) is one of the top four perennial forages worldwide and, despite its large economic advantages, often threatened by various environmental stresses. WRKY transcription factors (TFs) can regulate a variety of plant processes, widely participate in plant responses to biotic and abiotic stresses, and are one of the largest gene families in plants. WRKYs can usually bind W-box elements specifically. In this study, we identified a total of 93 DgWRKY genes and 281 RGAs, including 65, 169 and 47 nucleotide-binding site-leucine-rich repeats (NBS-LRRs), leucine-rich repeats receptor-like protein kinases (LRR-RLKs), and leucine-rich repeats receptor-like proteins (LRR-RLPs), respectively. Through analyzing the expression of DgWRKY genes in orchardgrass under different environmental stresses, it was found that many DgWRKY genes were differentially expressed under heat, drought, submergence, and rust stress. In particular, it was found that the greatest number of genes were differentially expressed under rust infection. Consistently, GO and KEGG enrichment analysis of all genes showed that 78 DgWRKY TFs were identified in the plant–pathogen interaction pathway, with 59 of them differentially expressed. Through cis-acting element prediction, 154 RGAs were found to contain W-box elements. Among them, DG6C02319.1 (a member of the LRR-RLK family) was identified as likely to interact with 14 DGWRKYs. Moreover, their expression levels in susceptible plants after rust inoculation were first up-regulated and then down-regulated, while those in the resistant plants were always up-regulated. In general, DgWRKYs responded to both biotic stress and abiotic stress. DgWRKYs and RGAs may synergistically respond to the response of orchardgrass to rust. This study provides meaningful insight into the molecular mechanisms of WRKY proteins in orchardgrass.

Comparative transcriptome analysis of R3a and Avr3a-mediated defense responses in transgenic tomato.

Late blight caused by Phytophthora infestans is one of the most devastating diseases in potatoes and tomatoes. At present, several late blight resistance genes have been mapped and cloned. To better understand the transcriptome changes during the incompatible interaction process between R3a and Avr3a, in this study, after spraying DEX, the leaves of MM-R3a-Avr3a and MM-Avr3a transgenic plants at different time points were used for comparative transcriptome analysis. A total of 7,324 repeated DEGs were detected in MM-R3a-Avr3a plants at 2-h and 6-h, and 729 genes were differentially expressed at 6-h compared with 2-h. Only 1,319 repeated DEGs were found in MM-Avr3a at 2-h and 6-h, of which 330 genes have the same expression pattern. Based on GO, KEGG and WCGNA analysis of DEGs, the phenylpropanoid biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were significantly up-regulated. Parts of the down-regulated DEGs were enriched in carbon metabolism and the photosynthesis process. Among these DEGs, most of the transcription factors, such as WRKY, MYB, and NAC, related to disease resistance or endogenous hormones SA and ET pathways, as well as PR, CML, SGT1 gene were also significantly induced. Our results provide transcriptome-wide insights into R3a and Avr3a-mediated incompatibility interaction.

Integrated small RNA, mRNA, and degradome sequencing reveals the important role of miRNAs in the interactions between parasitic plant Cuscuta australis and its host Trifolium repens

Cuscuta australis R.Br. is a stem parasite that obtains water and nutrients from host plants, with which it also exchanges proteins and mRNAs with host plants. Recently, a study found that novel miRNAs accumulated during C. campestris Yunk. parasitism of Arabidopsis thaliana L. However, the fate of miRNAs transferred from parasite to host plants as well as their targets has remained unexamined. To understand the miRNA–mRNA interaction network of host Trifolium repens L. in response to C. australis parasitism, integrated mRNA, small RNA, and degradome sequencing data were analyzed. In total, 60,824 unigenes were identified by RNA-seq, of which 1,601 were differentially expressed genes (DEGs). A total of 71 known miRNAs belonging to 38 miRNA families and 65 novel miRNAs were identified from small RNA sequencing data and 8,012 target genes were predicted. Of these target genes, 129 miRNA–mRNA pairs were identified via degradome analyzes. There were also eight differentially expressed miRNAs (DEMs). DEG and DEM correlation analyzes revealed 23 pairs of differentially expressed miRNA–mRNA pairs responsive to C. australis parasitism. The most enriched pathways were plant hormone signal transduction, ribosome and plant–pathogen interaction pathways. The miRNA–mRNA pairs in host T. repens, including trr-miR393a–RPS6, trr-miR398b–TGA, trr-miR395a/g–bHLH112, trr-miR395g–GH3, and trr-miRn41–WRKY/MYB, likely play important roles in interactions between host T. repens and parasitic C. australis. These results provide valuable information on the mechanisms of parasite–host plant interactions.