Histone Modifications Define Expression Bias Of Homoeologous Genomes In Allotetraploid And RNA-seq Of The Synthesis Tetraploid

The most widely-cultivated allotetraploid cotton(Gossypium hirsutum L.)is an excellent example of polyploidization and domestication from small trees into an annual crop.Genome doubling is predicted to have occurred at 1-2 million years ago(MYA)through hybridization and chromosome doubling between the extant progenitors that are closely related to G.arboreum(A2)or G.herbaceum(Al),originating in the Old World,and G.raimondii(D5),originating in the New World.Interestingly,the genome size of G.arboreum(1,746 Mb/1C)is almost twice the size of G raimondii(885Mb/1C),which is largely related to the expansion of transposable elements(TEs),including long terminal repeat(LTR)retrotransposons.The TE-rich regions often form heterochromatin,which are different from genic regions in the euchromatin.In this study,we investigated distribution patterns of histone modifications(H3K4me3 and H3K27me2)in heterochromatic and euchromatic regions of homoeologous chromosomes in G.hirsutum,which were quantified and comparatively analyzed with transcriptome data.The results have revealed distinctive patterns of heterochromatin and euchromatin between homoeologous chromosomes and an association of transcriptionally active chromatin with gene-rich regions.Although the overall fluorescent intensities of histone marks are equally distributed between A and D homoeologous chromosomes,the mean fluorescent intensities per chromosome bin of histone modifications linked to active transcription are significantly different between A and D homoeologs.ChIP-seq analysis further shows different numbers of A-and D-homoeologs with biased H3K4me3 levels among homoeologous pairs in the allotetraploid cotton,which correlate with the number and levels of expressed genes between A and D homoeologs.Two chromosomes display different expression levels relative to other chromosomes,probably because of translocations.These data indicate that both histone modifications and genome organization contribute to the expression bias of homoeologous genes in allopolyploids.Common wheat(Triticum aestivum L.)originated only about 10,000 years ago from hybridization event(s),most probably between a domesticated form of tetraploid wheat,T.turgidum(for example,ssp.durum or the more primitive ssp.parvicoccum,genome AABB)with a diploid goat grass species,Aegilops tauschii(genome DD).The genomes AADD have no extant(natural)counterpart is different from natural tetraploid wheat(AABB).Based on the analysis of transcriptome data,we found that the non additive gene expression mainly in low-regulated expression.Gene Ontology(GO)analysis showed enrichments low-regulated genes were mainly in the cell cycle chromatin modification,cell maturation,which is consistent with the chromosomal deletion,rearrangement and the instability of the karyotype in the synthesized AADD.This research provided experimental basis for the "transcriptome shock".Polyploidy is an important genomic feature for eukaryotes,especially many plants.The polyploidy brings genetic material for adaptive evolution.In this study,we found that both histone modifications and genome organization contribute to the expression bias of homoeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species including important crops.However,when increasing the dose of heterologous genes and genomes,polyploidy will face "transcription shock".If the abnormal expression of the critical biological path in polyploid that could not be adjusted,it may be unable to form a new species.