Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences,...

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Main Authors: Sarah Clark, Feng Yu, Lianfeng Gu, Xiang Jia Min
Format: Article
Language:English
Published: Frontiers Media S.A. 2019-05-01
Series:Frontiers in Plant Science
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fpls.2019.00689/full
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author Sarah Clark
Feng Yu
Lianfeng Gu
Xiang Jia Min
author_facet Sarah Clark
Feng Yu
Lianfeng Gu
Xiang Jia Min
author_sort Sarah Clark
collection DOAJ
description Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).
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spelling doaj.art-c6c79c0cb27049ccba0321d46efeef702022-12-22T02:58:41ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-05-011010.3389/fpls.2019.00689455538Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in TomatoSarah Clark0Feng Yu1Lianfeng Gu2Xiang Jia Min3Department of Biological Sciences, Youngstown State University, Youngstown, OH, United StatesDepartment of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, United StatesBasic Forestry and Proteomics Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, ChinaDepartment of Biological Sciences, Youngstown State University, Youngstown, OH, United StatesTomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).https://www.frontiersin.org/article/10.3389/fpls.2019.00689/fullalternative splicinggene expressiontomatomRNAplantSolanum lycopersicum
spellingShingle Sarah Clark
Feng Yu
Lianfeng Gu
Xiang Jia Min
Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato
Frontiers in Plant Science
alternative splicing
gene expression
tomato
mRNA
plant
Solanum lycopersicum
title Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato
title_full Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato
title_fullStr Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato
title_full_unstemmed Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato
title_short Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato
title_sort expanding alternative splicing identification by integrating multiple sources of transcription data in tomato
topic alternative splicing
gene expression
tomato
mRNA
plant
Solanum lycopersicum
url https://www.frontiersin.org/article/10.3389/fpls.2019.00689/full
work_keys_str_mv AT sarahclark expandingalternativesplicingidentificationbyintegratingmultiplesourcesoftranscriptiondataintomato
AT fengyu expandingalternativesplicingidentificationbyintegratingmultiplesourcesoftranscriptiondataintomato
AT lianfenggu expandingalternativesplicingidentificationbyintegratingmultiplesourcesoftranscriptiondataintomato
AT xiangjiamin expandingalternativesplicingidentificationbyintegratingmultiplesourcesoftranscriptiondataintomato