期刊论文详细信息
BMC Genomics
Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max
Research Article
Luis P. Iñiguez1  Mario Ramírez1  Georgina Hernández1  William B. Barbazuk2 
[1] Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico;Department of Biology, University of Florida, Gainesville, FL, USA;
关键词: Alternative splicing;    Conservation of alternative splicing;    RNA-seq;    Legumes;    Common bean;    Soybean;   
DOI  :  10.1186/s12864-017-4054-2
 received in 2017-02-06, accepted in 2017-08-11,  发布年份 2017
来源: Springer
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【 摘 要 】

BackgroundThe vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly available RNA-seq libraries, respectively, were analyzed.ResultsWe identified 85,570 AS events from P. vulgaris in 72% of expressed genes and 134,316 AS events in 70% of expressed genes from G. max. These were categorized in seven AS event types with intron retention being the most abundant followed by alternative acceptor and alternative donor, representing ~75% of all AS events in both plants. Conservation of AS events in homologous genes between the two species was analyzed where an overrepresentation of AS affecting 5’UTR regions was observed for certain types of AS events. The conservation of AS events was experimentally validated for 8 selected genes, through RT-PCR analysis. The different types of AS events also varied by relative position in the genes. The results were consistent in both species.ConclusionsThe identification and analysis of AS events are first steps to understand their biological relevance. The results presented here from two related legume species reveal high conservation, over ~15–20 MY of divergence, and may point to the biological relevance of AS.

【 授权许可】

CC BY   
© The Author(s). 2017

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