In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages
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Small interfering RNAs (siRNAs) are effectors of regulatory pathways underlying plant development, metabolism, and stress- and nutrient-signaling regulatory networks. The endogenous siRNAs are generally not conserved between plants; consequently, it is necessary and important to identify and characterize siRNAs from various plants. To address the nature and functions of siRNAs, and understand the biological roles of the huge siRNA population in grapevine (Vitis vinifera L.). The high-throughput sequencing technology was used to identify a large set of putative endogenous siRNAs from six grapevine tissues/organs. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to classify the target genes of siRNA. In total, 520,519 candidate siRNAs were identified and their expression profiles exhibited typical temporal characters during grapevine development. In addition, we identified two grapevine trans-acting siRNA (TAS) gene homologs (VvTAS3 and VvTAS4) and the derived trans-acting siRNAs (tasiRNAs) that could target grapevine auxin response factor (ARF) and myeloblastosis (MYB) genes. Furthermore, the GO and KEGG analysis of target genes showed that most of them covered a broad range of functional categories, especially involving in disease-resistance process. The large-scale and completely genome-wide level identification and characterization of grapevine endogenous siRNAs from the diverse tissues by high throughput technology revealed the nature and functions of siRNAs in grapevine.
KeywordsGrapevine Endogenous siRNA High-throughput Target genes
This research was supported by Project Funded by the Natural Science Foundation of China (NSFC) (Nos. 31672131, 31401846 and 31301759), China Postdoctoral Science Foundation Funded Project (2016M590465). Opening Project of State Key Laboratory of Crop Genetics and Germplasm Enhancement (ZW2014009).
Compliance with ethical standards
Conflict of interest
Xudong Zhu declares that he has no conflict of interest. Songtao Jiu declares that he has no conflict of interest. Xiaopeng Li declares that he has no conflict of interest. Kekun Zhang declares that he has no conflict of interest. Mengqi Wang declares that he has no conflict of interest. Chen Wang declares that he has no conflict of interest. Jinggui Fang declares that he has no conflict of interest.
This article does not contain any studies with human subjects or animals performed by any of the authors.
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