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Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops
BACKGROUND: Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578763/ https://www.ncbi.nlm.nih.gov/pubmed/26391769 http://dx.doi.org/10.1186/s12864-015-1914-5 |
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author | Min, Xiang Jia Powell, Brian Braessler, Jonathan Meinken, John Yu, Feng Sablok, Gaurav |
author_facet | Min, Xiang Jia Powell, Brian Braessler, Jonathan Meinken, John Yu, Feng Sablok, Gaurav |
author_sort | Min, Xiang Jia |
collection | PubMed |
description | BACKGROUND: Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms. RESULTS: We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions. CONCLUSIONS: AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1914-5) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4578763 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-45787632015-09-23 Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops Min, Xiang Jia Powell, Brian Braessler, Jonathan Meinken, John Yu, Feng Sablok, Gaurav BMC Genomics Research Article BACKGROUND: Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms. RESULTS: We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions. CONCLUSIONS: AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1914-5) contains supplementary material, which is available to authorized users. BioMed Central 2015-09-21 /pmc/articles/PMC4578763/ /pubmed/26391769 http://dx.doi.org/10.1186/s12864-015-1914-5 Text en © Min et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Min, Xiang Jia Powell, Brian Braessler, Jonathan Meinken, John Yu, Feng Sablok, Gaurav Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops |
title | Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops |
title_full | Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops |
title_fullStr | Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops |
title_full_unstemmed | Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops |
title_short | Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops |
title_sort | genome-wide cataloging and analysis of alternatively spliced genes in cereal crops |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578763/ https://www.ncbi.nlm.nih.gov/pubmed/26391769 http://dx.doi.org/10.1186/s12864-015-1914-5 |
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