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Functional characterization of plant small RNAs based on next-generation sequencing data

Paper ID Volume ID Publish Year Pages File Format Full-Text
15286 1400 2010 5 PDF Available
Title
Functional characterization of plant small RNAs based on next-generation sequencing data
Abstract

The currently developed next-generation sequencing (NGS) technology has significantly enhanced our capacity of small RNA (sRNA) exploration. Several ambitious sRNA projects have been established based on the technical support of NGS. Thanks to the high-throughput feature of NGS, huge amounts of sRNA sequencing data have been generated. However, much more research efforts are needed to further exploit these valuable data. In this study, we carried out functional analyses of sRNAs from 26 angiosperms by utilizing public sRNA NGS data. We proposed that the endogenous sRNAs largely represented by the 24-nt ones had a potential role in transposable element (TE) control in both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), based on the comparison of sRNA locus densities within the TEs to the non-TE genes. Functional analysis was performed for the predicted targets of the conserved sRNAs that were classified into eudicot-specific, monocot-specific, and angiosperm-conserved ones. Moreover, several miRNA families were found to be highly conserved, and miR396 was suggested to be the most conserved miRNA family between the eudicots and the monocots, indicating its essential role in angiosperm development. At last, we demonstrated that it was a great challenge for researchers to fully exploit these huge sRNA NGS datasets and numerous sRNA species remained to be uncovered and functionally characterized.

Keywords
Small RNA (sRNA); MicroRNA (miRNA); Functional characterization; Transposable element (TE) silencing; Angiosperm; Next-generation sequencing (NGS)
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Functional characterization of plant small RNAs based on next-generation sequencing data
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 34, Issues 5–6, December 2010, Pages 308–312
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us