Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

Abstract Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq)...

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Autores principales:	Qi You, Xin Yi, Kang Zhang, Chunchao Wang, Xuelian Ma, Xueyan Zhang, Wenying Xu, Fuguang Li, Zhen Su
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/870e8a2b093f40dfa23dcae369fb0d5f
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spelling	oai:doaj.org-article:870e8a2b093f40dfa23dcae369fb0d5f2021-12-02T11:40:58ZGenome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation10.1038/s41598-017-09680-62045-2322https://doaj.org/article/870e8a2b093f40dfa23dcae369fb0d5f2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-09680-6https://doaj.org/toc/2045-2322Abstract Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered in G. arboreum and G. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them between G. arboreum and G. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.Qi YouXin YiKang ZhangChunchao WangXuelian MaXueyan ZhangWenying XuFuguang LiZhen SuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qi You Xin Yi Kang Zhang Chunchao Wang Xuelian Ma Xueyan Zhang Wenying Xu Fuguang Li Zhen Su Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
description	Abstract Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered in G. arboreum and G. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them between G. arboreum and G. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.
format	article
author	Qi You Xin Yi Kang Zhang Chunchao Wang Xuelian Ma Xueyan Zhang Wenying Xu Fuguang Li Zhen Su
author_facet	Qi You Xin Yi Kang Zhang Chunchao Wang Xuelian Ma Xueyan Zhang Wenying Xu Fuguang Li Zhen Su
author_sort	Qi You
title	Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
title_short	Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
title_full	Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
title_fullStr	Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
title_full_unstemmed	Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
title_sort	genome-wide comparative analysis of h3k4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/870e8a2b093f40dfa23dcae369fb0d5f
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Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

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