High-Throughput Sequencing Identifies Novel and Conserved Cucumber (Cucumis sativus L.) microRNAs in Response to Cucumber Green Mottle Mosaic Virus Infection

H W Liu; L X Luo; C Q Liang; N Jiang; P F Liu; J Q Li

doi:10.1371/journal.pone.0129002

High-Throughput Sequencing Identifies Novel and Conserved Cucumber (Cucumis sativus L.) microRNAs in Response to Cucumber Green Mottle Mosaic Virus Infection

PLoS One. 2015 Jun 15;10(6):e0129002. doi: 10.1371/journal.pone.0129002. eCollection 2015.

Authors

H W Liu¹, L X Luo², C Q Liang², N Jiang², P F Liu², J Q Li²

Affiliations

¹ Department of Plant Pathology/Key Laboratory of Plant Pathology, China Agricultural University, Beijing, People's Republic of China; Beijing Engineering Research Centre of Seed and Plant Health/Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, People's Republic of China; Molecular Plant Pathology Laboratory, United States Department-Agricultural Research Service, Beltsville, Maryland, United States of America.
² Department of Plant Pathology/Key Laboratory of Plant Pathology, China Agricultural University, Beijing, People's Republic of China; Beijing Engineering Research Centre of Seed and Plant Health/Beijing Key Laboratory of Seed Disease Testing and Control, Beijing, People's Republic of China.

Abstract

Seedlings of Cucumis sativus L. (cv. 'Zhongnong 16') were artificially inoculated with Cucumber green mottle mosaic virus (CGMMV) at the three-true-leaf stage. Leaf and flower samples were collected at different time points post-inoculation (10, 30 and 50 d), and processed by high throughput sequencing analysis to identify candidate miRNA sequences. Bioinformatic analysis using screening criteria, and secondary structure prediction, indicated that 8 novel and 23 known miRNAs (including 15 miRNAs described for the first time in vivo) were produced by cucumber plants in response to CGMMV infection. Moreover, gene expression profiles (p-value <0.01) validated the expression of 3 of the novel miRNAs and 3 of the putative candidate miRNAs and identified a further 82 conserved miRNAs in CGMMV-infected cucumbers. Gene ontology (GO) analysis revealed that the predicted target genes of these 88 miRNAs, which were screened using the psRNATarget and miRanda algorithms, were involved in three functional categories: 2265 in molecular function, 1362 as cellular components and 276 in biological process. The subsequent Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the predicted target genes were frequently involved in metabolic processes (166 pathways) and genetic information processes (40 pathways) and to a lesser degree the biosynthesis of secondary metabolites (12 pathways). These results could provide useful clues to help elucidate host-pathogen interactions in CGMMV and cucumber, as well as for the screening of resistance genes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Cucumis sativus / genetics
Cucumis sativus / immunology
Cucumis sativus / virology*
Disease Resistance / genetics
High-Throughput Nucleotide Sequencing
MicroRNAs / chemistry
MicroRNAs / genetics
MicroRNAs / metabolism*
Oligonucleotide Array Sequence Analysis
Plant Diseases / genetics*
Plant Diseases / immunology
Plant Diseases / virology
RNA, Plant / chemistry
RNA, Plant / genetics
RNA, Plant / metabolism*
Sequence Analysis, RNA
Tobamovirus / physiology*

Substances

MicroRNAs
RNA, Plant

Grants and funding

This work was supported by the National Science Foundation of China (NSFC) project (Grant No. 31371910), the Program for Changjiang Scholars and Innovative Research Team in University (Grant No. IRT1042) and the Special Fund for Agroscientific Research in the Public Interest of China (Grant No. 201303028). All the funding was received by Dr. Jianqiang Li. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.