Long non-coding RNAs as molecular players in plant defense against pathogens

Zaynab, Madiha; Fatima, Mahpara; Abbas, Safdar; Umair, Muhammad; Sharif, Yasir; Raza, Muhammad Ammar

doi:10.1016/j.micpath.2018.05.050

Cited by 34 publications

(25 citation statements)

References 27 publications

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“…Host lncRNAs also play roles in plant defence. In response to pathogen infection, lncRNA-dependent immune systems protect host plants via lncRNAs' regulation of pathogen-associated molecular patterns (PAMPs) and other effectors (Zaynab et al, 2018). Arabidopsis cells secrete exosome-like extracellular vesicles to deliver small RNAs (sRNAs) into B. cinerea to silence fungal genes critical for pathogenicity, indicating that Arabidopsis has employed exosome-mediated cross-kingdom RNA interference as part of its immune responses during the evolutionary arms race with the pathogen (Cai et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection‐related development and host penetration

Zhang

Sun

Liu

et al. 2020

Molecular Plant Pathology

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Section: Introductionmentioning

confidence: 99%

Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection‐related development and host penetration

Zhang

Sun

Liu

et al. 2020

Molecular Plant Pathology

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“…These numbers are likely to be higher if both a larger variety of RNA-seq samples is used for the annotation and software specifically designed for element prediction are used. Nevertheless, our annotations can be used to explore long non-coding RNAs that may be involved in key biological processes in plants (Liu et al 2012;Zaynab et al 2018). Of the 21,661 protein coding genes, 83% had an InterProScan match and 76% were assigned to COGs (clusters of orthologous groups) by eggNOG-mapper (Table 4).…”

Section: Annotation Of the Genome Draft Reference Sequencementioning

confidence: 99%

A high-quality cucumber genome assembly enhances computational comparative genomics

et al. 2019

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Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data from three individuals to analyse the polymorphisms. Using this approach, we uncovered differentiation aspects in the genomes of the inbred B10 line. The newly assembled genome sequence (B10v3) has the highest contiguity and quality characteristics among the currently available cucumber genome draft sequences. Standard and newly designed approaches were used to predict single nucleotide and structural variants that were unique among the three individual genomes. Some of the variant predictions spanned protein-coding genes and their promoters, and some were in the neighbourhood of annotated interspersed repetitive elements, indicating that the highly inbred homozygous plants remained genetically dynamic. This is the first bioinformatic comparative genomics study of a single highly inbred plant line. For this project, we developed a polymorphism prediction method with optimized precision parameters, which allowed the effective detection of small nucleotide variants (SNVs). This methodology could significantly improve bioinformatic pipelines for comparative genomics and thus has great practical potential in genomic metadata handling.

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“…Furthermore, many studies reported that lncRNAs play important roles in plant defense against pathogens [66][67][68]. In tomato, a plausible model for TYLCV-induced diseases and host antiviral immunity was uncovered; that is, lncRNAs interact with the IR-derived vsRNAs to control disease development during TYLCV infection, which provide an effective strategy for the control of plant viral pathogens [67].…”

Section: Discussionmentioning

confidence: 99%

Discovery, Identification, and Functional Characterization of Long Noncoding RNAs in Arachis hypogaea L.

Tian

Feng

Zhang

et al. 2020

Preprint

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Abstract Background Long noncoding RNAs (lncRNAs), which are typically >200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. Results A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1,442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. The majority of the lncRNAs featured an exon/intron structure, and approximately 44.17% were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. Conclusions This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

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Long non-coding RNAs as molecular players in plant defense against pathogens

Cited by 34 publications

References 27 publications

Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection‐related development and host penetration

Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection‐related development and host penetration

A high-quality cucumber genome assembly enhances computational comparative genomics

Discovery, Identification, and Functional Characterization of Long Noncoding RNAs in Arachis hypogaea L.

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