{"title":"Identification and Analysis of Alternative Splicing in Soybean Plants","authors":"X. Min, Theoni Kasamias, Mykaela Wagner, Atinuke Ogunbayi, Feng Yu","doi":"10.29007/2qv6","DOIUrl":null,"url":null,"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.","PeriodicalId":93549,"journal":{"name":"EPiC series in computing","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"2","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"EPiC series in computing","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.29007/2qv6","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 2
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.