Genome-wide analysis of small RNA and novel microRNA discovery during fiber and seed initial development in Gossypium hirsutum. L

Hua Zhang; Qun Wan; Wenxue Ye; Yuanda Lv; Huaitong Wu; Tianzhen Zhang

doi:10.1371/journal.pone.0069743

Genome-wide analysis of small RNA and novel microRNA discovery during fiber and seed initial development in Gossypium hirsutum. L

PLoS One. 2013 Jul 29;8(7):e69743. doi: 10.1371/journal.pone.0069743. Print 2013.

Authors

Hua Zhang¹, Qun Wan, Wenxue Ye, Yuanda Lv, Huaitong Wu, Tianzhen Zhang

Affiliation

¹ National Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Center/the Ministre of Education, Cotton Research Institute, Nanjing Agricultural University, Nanjing, China.

Abstract

Cotton is the source of the most important, renewable natural textile fiber and oil in the world. MicroRNAs (miRNAs) are endogenous, non-coding, approximately 18-24 nucleotides long RNAs and function in the negative regulation of their target genes. Two mostly overlapping libraries of small RNA molecules were constructed and sequenced, and served as repetition sets of data to identify miRNAs involved in fiber initiation and seed development. The D genome sequence of Gossypium raimondii was used in conjunction with EST sequences to predict miRNA precursors. Overall, 93 new miRNA precursors were identified, of which 28 belonged to 10 known families and the other 65 were considered to be novel miRNAs. Seven hundred EST sequences were proposed to be candidate target genes which involved in the regulation of a diverse group of genes with diverse functions and transcription factors. Some of the novel miRNAs and candidate target genes were validated by the Northern blot and rapid amplification of 5' cDNA ends (5' RACE).

Publication types

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

MeSH terms

Gene Expression Regulation, Plant
Gossypium / genetics*
MicroRNAs / genetics*
RNA, Plant / genetics*
Seeds / metabolism*
Sequence Analysis, RNA

Substances

MicroRNAs
RNA, Plant

Grants and funding

This work was financially supported in part by grants from the State Basic Research Development Program of China (973 Program) (2011CB109300) and the Priority Academic Program Development of Jiangsu Higher Education Institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.