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Open Access Research article

RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications

Lei Wang1, Chenlong Cao1, Qibin Ma34, Qiaoying Zeng34, Haifeng Wang12, Zhihao Cheng1, Genfeng Zhu12, Ji Qi12, Hong Ma125, Hai Nian34* and Yingxiang Wang1*

Author Affiliations

1 State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China

2 Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China

3 State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642 Guangzhou, China

4 Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642 Guangzhou, China

5 Institute of Biodiversity Sciences, Fudan University, 200433 Shanghai, China

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BMC Plant Biology 2014, 14:169  doi:10.1186/1471-2229-14-169

Published: 17 June 2014

Abstract

Background

Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited.

Results

In this study, we employed RNA-seq to investigate transcriptomes of 11 soybean tissues, for genome-wide discovery of truly expressed genes, and novel and alternative transcripts, as well as analyses of conservation and divergence of duplicated genes and their functional implications. We detected a total of 54,132 high-confidence expressed genes, and identified 6,718 novel transcriptional regions with a mean length of 372 bp. We also provided strong evidence for alternative splicing (AS) events for ~15.9% of the genes with two or more exons. Among them, 1,834 genes exhibited stage-dependent AS, and 202 genes had tissue-biased exon-skipping events. We further defined the conservation and divergence in expression patterns between duplicated gene pairs from recent whole genome duplications (WGDs); differentially expressed genes, tissue preferentially expressed genes, transcription factors and specific gene family members were identified for shoot apical meristem and flower development.

Conclusions

Our results significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean.

Keywords:
Soybean; RNA-seq; Transcriptome; Novel transcriptional regions; Alternative splicing; Meristem; Transcription factors