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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...

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Autores principales: Wang, Lei, Cao, Chenlong, Ma, Qibin, Zeng, Qiaoying, Wang, Haifeng, Cheng, Zhihao, Zhu, Genfeng, Qi, Ji, Ma, Hong, Nian, Hai, Wang, Yingxiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
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.
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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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