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

BMC Plant Biology

Research Article

Hai Nian¹  Qibin Ma¹  Qiaoying Zeng¹  Lei Wang²  Chenlong Cao²  Yingxiang Wang²  Zhihao Cheng²  Haifeng Wang³  Genfeng Zhu³  Ji Qi³  Hong Ma⁴ 

[1] State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642, Guangzhou, China;Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642, Guangzhou, China;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;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;Institute of Biomedical Sciences, Fudan University, 200032, Shanghai, China;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;Institute of Biomedical Sciences, Fudan University, 200032, Shanghai, China;Institute of Biodiversity Sciences, Fudan University, 200433, Shanghai, China;

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

DOI  :  10.1186/1471-2229-14-169

 received in 2014-04-05, accepted in 2014-06-05,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundSoybean 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.ResultsIn 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© Wang et al.; licensee BioMed Central Ltd. 2014