Open AccessIdentification and Analysis of Alternative Splicing in Soybean Plants
Author(s) -
Xiang Jia Min,
Theoni Kasamias,
Mykaela Wagner,
Atinuke Ogunbayi,
Feng Ye
Publication year - 2022
Publication title -
epic series in computing
Language(s) - English
Resource type - Conference proceedings
SCImago Journal Rank - 0.21
H-Index - 7
ISSN - 2398-7340
DOI - 10.29007/2qv6
Subject(s) - intron , biology , genome , rna splicing , gene , computational biology , alternative splicing , proteome , transcriptome , exon , expressed sequence tag , genetics , identification (biology) , rna , botany , gene expression
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.