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RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
BACKGROUND: Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070088/ https://www.ncbi.nlm.nih.gov/pubmed/24939556 http://dx.doi.org/10.1186/1471-2229-14-169 |
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author | Wang, Lei Cao, Chenlong Ma, Qibin Zeng, Qiaoying Wang, Haifeng Cheng, Zhihao Zhu, Genfeng Qi, Ji Ma, Hong Nian, Hai Wang, Yingxiang |
author_facet | Wang, Lei Cao, Chenlong Ma, Qibin Zeng, Qiaoying Wang, Haifeng Cheng, Zhihao Zhu, Genfeng Qi, Ji Ma, Hong Nian, Hai Wang, Yingxiang |
author_sort | Wang, Lei |
collection | PubMed |
description | BACKGROUND: Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited. RESULTS: In this study, we employed RNA-seq to investigate transcriptomes of 11 soybean tissues, for genome-wide discovery of truly expressed genes, and novel and alternative transcripts, as well as analyses of conservation and divergence of duplicated genes and their functional implications. We detected a total of 54,132 high-confidence expressed genes, and identified 6,718 novel transcriptional regions with a mean length of 372 bp. We also provided strong evidence for alternative splicing (AS) events for ~15.9% of the genes with two or more exons. Among them, 1,834 genes exhibited stage-dependent AS, and 202 genes had tissue-biased exon-skipping events. We further defined the conservation and divergence in expression patterns between duplicated gene pairs from recent whole genome duplications (WGDs); differentially expressed genes, tissue preferentially expressed genes, transcription factors and specific gene family members were identified for shoot apical meristem and flower development. CONCLUSIONS: Our results significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean. |
format | Online Article Text |
id | pubmed-4070088 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40700882014-06-26 RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications Wang, Lei Cao, Chenlong Ma, Qibin Zeng, Qiaoying Wang, Haifeng Cheng, Zhihao Zhu, Genfeng Qi, Ji Ma, Hong Nian, Hai Wang, Yingxiang BMC Plant Biol Research Article BACKGROUND: Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited. RESULTS: In this study, we employed RNA-seq to investigate transcriptomes of 11 soybean tissues, for genome-wide discovery of truly expressed genes, and novel and alternative transcripts, as well as analyses of conservation and divergence of duplicated genes and their functional implications. We detected a total of 54,132 high-confidence expressed genes, and identified 6,718 novel transcriptional regions with a mean length of 372 bp. We also provided strong evidence for alternative splicing (AS) events for ~15.9% of the genes with two or more exons. Among them, 1,834 genes exhibited stage-dependent AS, and 202 genes had tissue-biased exon-skipping events. We further defined the conservation and divergence in expression patterns between duplicated gene pairs from recent whole genome duplications (WGDs); differentially expressed genes, tissue preferentially expressed genes, transcription factors and specific gene family members were identified for shoot apical meristem and flower development. CONCLUSIONS: Our results significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean. BioMed Central 2014-06-17 /pmc/articles/PMC4070088/ /pubmed/24939556 http://dx.doi.org/10.1186/1471-2229-14-169 Text en Copyright © 2014 Wang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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 Wang, Lei Cao, Chenlong Ma, Qibin Zeng, Qiaoying Wang, Haifeng Cheng, Zhihao Zhu, Genfeng Qi, Ji Ma, Hong Nian, Hai Wang, Yingxiang RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications |
title | RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications |
title_full | RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications |
title_fullStr | RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications |
title_full_unstemmed | RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications |
title_short | RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications |
title_sort | rna-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070088/ https://www.ncbi.nlm.nih.gov/pubmed/24939556 http://dx.doi.org/10.1186/1471-2229-14-169 |
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