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Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing.
- Source :
-
Journal of basic microbiology [J Basic Microbiol] 2018 Mar; Vol. 58 (3), pp. 227-237. Date of Electronic Publication: 2017 Dec 07. - Publication Year :
- 2018
-
Abstract
- RNA interference (RNAi) is a conserved mechanism against viruses in plants and animals. It is thought to inactivate the viral genome by producing virus-derived small interfering RNAs (vsiRNAs). Rice black-streaked dwarf virus (RBSDV) is transmitted to plants by the small brown planthopper (Laodelphax striatellus), and seriously threatens production of rice in East Asia, particularly Oryza sativa japonica subspecies. Through deep sequencing, genome-wide comparisons of RBSDV-derived vsiRNAs were made between the japonica variety Nipponbare, and the indica variety 9311. Four small RNA libraries were constructed from the leaves and shoots of each variety. We found 659,756 unique vsiRNAs in the four samples, and only 43,485 reads were commonly shared. The size distributions of vsiRNAs were mostly 21- and 22-nt long, and A/U bias (66-68%) existed at the first nucleotide of vsiRNAs. Additionally, vsiRNAs were continuously but heterogeneously distributed along S1-S10 segments of the RBSDV genome. Distribution profiles of vsiRNA hotspots were similar in different hosts and tissues, and the 5'- and 3'-terminal regions of S4, S5, and S8 had more hotspots. Distribution and abundance of RBSDV vsiRNAs could be useful in designing efficient targets for exploiting RNA interference for virus resistance. Degradome analysis found 25 and 11 host genes appeared to be targeted by vsiRNAs in 9311 and Nipponbare. We report for the first time vsiRNAs derived from RBSDV-infected rice.<br /> (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Subjects :
- High-Throughput Nucleotide Sequencing
Plant Leaves virology
Plant Shoots virology
RNA Interference
RNA, Small Interfering genetics
RNA, Viral genetics
Host-Pathogen Interactions
Oryza genetics
Oryza virology
Plant Viruses genetics
Plant Viruses growth & development
RNA, Small Interfering analysis
RNA, Viral analysis
Subjects
Details
- Language :
- English
- ISSN :
- 1521-4028
- Volume :
- 58
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- Journal of basic microbiology
- Publication Type :
- Academic Journal
- Accession number :
- 29215744
- Full Text :
- https://doi.org/10.1002/jobm.201700325