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.
Highlights
Chromatin is an instructive DNA scaffold that can respond to external conditions and can be modulated through the modification of histones to change DNA accessibility and gene expression[1]
According to the quality control, the mapped ratios of three H3K4me[3] histone ChIP-seq samples were all above 90%, which indicates that the data should be reliable (Table 1)
Total peaks of histone modification deposition and the number of these peaks related to different genomic regions were calculated (Table 1)
Summary
Chromatin is an instructive DNA scaffold that can respond to external conditions and can be modulated through the modification of histones to change DNA accessibility and gene expression[1]. H3K4me[3] histones are associated with transcription start sites (TSS) of expressed genes[9] and are usually located from ∼150 bp upstream of the TSS to ∼500 bp downstream in rice[10]. Due to these characteristics, H3K4me[3] has been widely used for plant biology research. Available omics data increased explosively with the publication of the diploid and allotetraploid cotton genomes, which makes heterosis research at multi-dimensional levels (transcriptome and epigenome) more efficient in studying cotton’s evolution[18,19,20,21]. We developed a platform named MOAP (http://structuralbiology.cau.edu.cn/MOAP/) for novel transcript browsing and searching
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