Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

Feng, Shan; Fang, Hongcheng; Liu, Xia; Dong, Yixin; Wang, Qingpeng; Yang, Ke Qiang

doi:10.1186/s12864-020-07310-6

Cited by 31 publications

(37 citation statements)

References 67 publications

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“…The N gene of tobacco ( Nicotiana tabacum ) is a typical R gene engendering the localization of tobacco mosaic virus (TMV) infection and the elicitation of a hypersensitive necrotic response [ 50 ]. In addition, three hub potential R genes (G-type lectin S-receptor-like serine/threonine-protein kinase LECRK1, LOC108979712 ; probably inactive leucine-rich repeat receptor-like protein kinase At2g25790, LOC109009481 ; and TMV resistance protein N-like, LOC108988638 ) obtained in the study of Feng et al [ 29 ] also present in the WGCNA module in this study. Therefore, the roles of these potential R genes in walnut resistance to anthracnose were worth further study.…”

Section: Discussionsupporting

confidence: 65%

“…1 c, f, i, l), and distal uninoculated tissues access to the resistance at 120 hpi. Thus, according to the lifestyle transitions of C. gloeosporioides , the resistant fruits (F26) and susceptible fruits (F423) were collected and inoculated according to the description by Feng et al [ 29 ]. The fruit bract tissues of F26 and F423 at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi were used for the transcriptome and proteome analysis.…”

Section: Resultsmentioning

confidence: 99%

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Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides

et al. 2021

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Background Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease affecting walnut production. The resistance of walnut fruit to C. gloeosporioides is a highly complicated and genetically programmed process. However, the underlying mechanisms have not yet been elucidated. Results To understand the molecular mechanism underlying the defense of walnut to C. gloeosporioides, we used RNA sequencing and label-free quantitation technologies to generate transcriptomic and proteomic profiles of tissues at various lifestyle transitions of C. gloeosporioides, including 0 hpi, pathological tissues at 24 hpi, 48 hpi, and 72 hpi, and distal uninoculated tissues at 120 hpi, in anthracnose-resistant F26 fruit bracts and anthracnose-susceptible F423 fruit bracts, which were defined through scanning electron microscopy. A total of 21,798 differentially expressed genes (DEGs) and 1929 differentially expressed proteins (DEPs) were identified in F26 vs. F423 at five time points, and the numbers of DEGs and DEPs were significantly higher in the early infection stage. Using pairwise comparisons and weighted gene co-expression network analysis of the transcriptome, we identified two modules significantly related to disease resistance and nine hub genes in the transcription expression gene networks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of the DEGs and DEPs revealed that many genes were mainly related to immune response, plant hormone signal transduction, and secondary metabolites, and many DEPs were involved in carbon metabolism and photosynthesis. Correlation analysis between the transcriptome data and proteome data also showed that the consistency of the differential expression of the mRNA and corresponding proteins was relatively higher in the early stage of infection. Conclusions Collectively, these results help elucidate the molecular response of walnut fruit to C. gloeosporioides and provide a basis for the genetic improvement of walnut disease resistance.

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Section: Discussionsupporting

confidence: 65%

Section: Resultsmentioning

confidence: 99%

Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides

et al. 2021

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“…To analyze the expression levels of WRKY in common walnut, 17 transcriptome data were downloaded, including a total of 17 tissues from PJ Martínez-García et al, 2016 (PRJNA291087) [ 51 ], 10 anthracnose-resistant F26 fruits from the B26 clone (AR) and 10 anthracnose-susceptible F423 fruits from the 4–23 clone (AS) of walnut [ 52 ] (PRJNA612972) ( Table S1 ). Cufflinks was used to [ 53 ] to quantify these gene expression levels based on fragments per million base readings per million mapped read (FPKM) values with default parameters, and expression level was calculated using Hemi 1.0 software with default parameters [ 54 ].…”

Section: Methodsmentioning

confidence: 99%

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

Fan

Zhou

et al. 2021

Genes

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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.

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“…Genes related to the salicylic acid-mediated defence process were co-expressed with lncRNAs in kiwifruit plant challenged with the bacteria P. syringae . Likewise, lncRNAs of resistant walnuts to C. gloeosporioides were predicted to trans-regulate genes involved in defence pathways of the jasmonic acid and auxins (Feng et al 2021).…”

Section: Discussionmentioning

confidence: 99%

“…In kiwifruit leaves infected by P. syringae, a weighted gene co-expression network analysis revealed a number of lncRNAs closely related to plant immune response and signal transduction . Likewise, Feng et al (2021) identified 14,525 lncRNAs related to the walnut anthracnose resistance. This analysis showed that the target genes of the up-regulated lncRNAs were enriched in immune-related processes during the infection of the causal agent Colletotrichum gloeosporioides.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Fusarium circinatum-Responsive lncRNAs in Pinus radiata

Zamora-Ballesteros

Martín‐García

Suárez-Vega

2021

Preprint

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One of the most promising strategies of Pine Pitch Canker (PPC) management is the use of reproductive plant material resistant to the disease. Understanding the complexity of plant transcriptome that underlies the defence to the causal agent Fusarium circinatum, would greatly facilitate the development of an accurate breeding program. Long non-coding RNAs (lncRNAs) are emerging as important transcriptional regulators under biotic stresses in plants. However, to date, characterization of lncRNAs in conifer trees has not been reported. In this study, transcriptomic identification of lncRNAs was carried out using strand-specific paired-end RNA sequencing, from Pinus radiata samples inoculated with F. circinatum at an early stage of infection. Overall, 13,312 lncRNAs were predicted through a bioinformatics approach, including long intergenic non-coding RNAs (92.3%), antisense lncRNAs (3.3%) and intronic lncRNAs (2.9%). Compared with protein-coding RNAs, pine lncRNAs are shorter, have lower expression, lower GC content and harbour fewer and shorter exons. A total of 164 differentially expressed (DE) lncRNAs were identified in response to F. circinatum infection in the inoculated versus mock-inoculated P. radiata seedlings. The predicted cis-regulated target genes of these pathogen-responsive lncRNAs were related to defence mechanisms such as kinase activity, phytohormone regulation, and cell wall reinforcement. Co-expression network analysis of DE lncRNAs, DE protein-coding RNAs and lncRNA target genes also indicated a potential network regulating pectinesterase activity and cell wall remodelling. This study presents the first analysis of conifer lncRNAs involved in the regulation of defence network and provides the basis for future functional characterizations of lncRNAs in relation to pine defence responses against F. circinatum.

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Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

Cited by 31 publications

References 67 publications

Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides

Transcriptome and proteome analysis of walnut (Juglans regia L.) fruit in response to infection by Colletotrichum gloeosporioides

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

Genome-Wide Identification and Characterization of Fusarium circinatum-Responsive lncRNAs in Pinus radiata

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