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Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton

Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcri...

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Autores principales: Wang, Kun, Wang, Dehe, Zheng, Xiaomin, Qin, Ai, Zhou, Jie, Guo, Boyu, Chen, Yanjun, Wen, Xingpeng, Ye, Wen, Zhou, Yu, Zhu, Yuxian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797763/
https://www.ncbi.nlm.nih.gov/pubmed/31624240
http://dx.doi.org/10.1038/s41467-019-12575-x
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author Wang, Kun
Wang, Dehe
Zheng, Xiaomin
Qin, Ai
Zhou, Jie
Guo, Boyu
Chen, Yanjun
Wen, Xingpeng
Ye, Wen
Zhou, Yu
Zhu, Yuxian
author_facet Wang, Kun
Wang, Dehe
Zheng, Xiaomin
Qin, Ai
Zhou, Jie
Guo, Boyu
Chen, Yanjun
Wen, Xingpeng
Ye, Wen
Zhou, Yu
Zhu, Yuxian
author_sort Wang, Kun
collection PubMed
description Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.
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spelling pubmed-67977632019-10-21 Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton Wang, Kun Wang, Dehe Zheng, Xiaomin Qin, Ai Zhou, Jie Guo, Boyu Chen, Yanjun Wen, Xingpeng Ye, Wen Zhou, Yu Zhu, Yuxian Nat Commun Article Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community. Nature Publishing Group UK 2019-10-17 /pmc/articles/PMC6797763/ /pubmed/31624240 http://dx.doi.org/10.1038/s41467-019-12575-x Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Wang, Kun
Wang, Dehe
Zheng, Xiaomin
Qin, Ai
Zhou, Jie
Guo, Boyu
Chen, Yanjun
Wen, Xingpeng
Ye, Wen
Zhou, Yu
Zhu, Yuxian
Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton
title Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton
title_full Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton
title_fullStr Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton
title_full_unstemmed Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton
title_short Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton
title_sort multi-strategic rna-seq analysis reveals a high-resolution transcriptional landscape in cotton
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797763/
https://www.ncbi.nlm.nih.gov/pubmed/31624240
http://dx.doi.org/10.1038/s41467-019-12575-x
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