Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max

• Published in: BMC genomics Vol. 18; no. 1; p. 650
• Main Authors: Iñiguez, Luis P, Ramírez, Mario, Barbazuk, William B, Hernández, Georgina
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 22.08.2017; BioMed Central
• Subjects: Alternative splicing; Alternative Splicing - genetics; Animals; Biological effects; Common beans; Conservation; Conserved Sequence; Divergence; Expressed sequence tags; Gene Expression Regulation, Plant; Gene sequencing; Genes; Genetic aspects; Genetic engineering; Genomes; Genomics; Glycine max; Glycine max - genetics; Homology; Identification; Identification and classification; Isoforms; Legumes; Leguminous plants; Localization; Nitrogen; Nucleotide sequence; Phaseolus - genetics; Phaseolus vulgaris; Polymerase chain reaction; Proteins; Retention; Ribonucleic acid; RNA; Soybean; Species; Splicing; Transcription; Wildlife conservation; Alternative splicing; Legumes; Common bean; Soybean; RNA-seq; Conservation of alternative splicing
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-017-4054-2

The 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. We 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. The 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.