Identification and Analysis of Alternative Splicing in Soybean Plants

Abstract

Alternative splicing (AS) increases the diversities of transcriptomes and proteomes in plants. The work reports identification and analysis of genes and their transcripts with a focus on AS in soybean plants by integrating mapping information of over 1.5 million of mRNAs and expressed sequence tags (ESTs) with more than 6 billons of mapped reads collected from 90 RNA-seq datasets obtained from multiple experiments. A total of 294,164 AS events were detected and categorized into basic events (151,710, 51.57%) and complex events (142,454, 48.43%). The basic AS events include intron retention (18.52%), alternative acceptor sites (16.33%), alternative donor site (8.99%), and exon skipping (7.73%). The AS rate in intron containing genes was estimated to be ~56.3% in soybean based on the current analysis. In addition, a total of 41,453 new genomic loci, which were not previously annotated in the genome, were detected by mapping transcripts to the genome. The annotated data can be accessed through a public database for searching and downloading. This work provides a resource for further detailed functional analysis of gene products in soybean plants.