De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana

Guodong Rao; Jinkai Sui; Yanfei Zeng; Caiyun He; Aiguo Duan; Jianguo Zhang

doi:10.1371/journal.pone.0109122

De novo transcriptome and small RNA analysis of two Chinese willow cultivars reveals stress response genes in Salix matsudana

PLoS One. 2014 Oct 2;9(10):e109122. doi: 10.1371/journal.pone.0109122. eCollection 2014.

Authors

Guodong Rao¹, Jinkai Sui¹, Yanfei Zeng², Caiyun He², Aiguo Duan², Jianguo Zhang²

Affiliations

¹ Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China.
² State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, Republic of China.

Abstract

Salix matsudana Koidz. is a deciduous, rapidly growing, and drought resistant tree and is one of the most widely distributed and commonly cultivated willow species in China. Currently little transcriptomic and small RNAomic data are available to reveal the genes involve in the stress resistant in S. matsudana. Here, we report the RNA-seq analysis results of both transcriptome and small RNAome data using Illumina deep sequencing of shoot tips from two willow variants(Salix. matsudana and Salix matsudana Koidz. cultivar 'Tortuosa'). De novo gene assembly was used to generate the consensus transcriptome and small RNAome, which contained 106,403 unique transcripts with an average length of 944 bp and a total length of 100.45 MB, and 166 known miRNAs representing 35 miRNA families. Comparison of transcriptomes and small RNAomes combined with quantitative real-time PCR from the two Salix libraries revealed a total of 292 different expressed genes(DEGs) and 36 different expressed miRNAs (DEMs). Among the DEGs and DEMs, 196 genes and 24 miRNAs were up regulated, 96 genes and 12 miRNA were down regulated in S. matsudana. Functional analysis of DEGs and miRNA targets showed that many genes were involved in stress resistance in S. matsudana. Our global gene expression profiling presents a comprehensive view of the transcriptome and small RNAome which provide valuable information and sequence resources for uncovering the stress response genes in S. matsudana. Moreover the transcriptome and small RNAome data provide a basis for future study of genetic resistance in Salix.

Publication types

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

MeSH terms

RNA, Plant / genetics*
Salix / genetics*
Stress, Physiological / genetics*
Transcriptome*

Substances

RNA, Plant

Grants and funding

The research was sponsored by grants from the National Natural Science Foundation of China (31400569), the Fundamental Research Funds for the Central Non-profit Research Institution of CAF (RIF2013-11), Beijing Co-building Plan for Scientific Research and Postgraduate Education (2013K0140, 2013K0141, 2014K0151, 2014K0152), and Collaborative Innovation Plan of Jiangsu Higher Education. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.