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An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses

ABSTRACT: Wheat (Triticum aestivum) has a large allohexaploid genome. Subgenome-divergent regulation contributed to genome plasticity and the domestication of polyploid wheat. However, the specificity encoded in the wheat genome determining subgenome-divergent spatio-temporal regulation has been largely unexplored. The considerable size and complexity of the genome are major obstacles to dissecting the regulatory specificity. Here, we compared the epigenomes and transcriptomes from a large set of samples under diverse developmental and environmental conditions. Thousands of distal epigenetic regulatory elements (distal-epiREs) were specifically linked to their target promoters with coordinated epigenomic changes. We revealed that subgenome-divergent activity of homologous regulatory elements are affected by specific epigenetic signatures. Subgenome-divergent epiRE regulation of tissue specificity is associated with dynamic modulation of H3K27me3 mediated by Polycomb complex and demethylases. Furthermore, quantitative epigenomic approaches detected key stress responsive cis- and trans-acting factors validated by DNA Affinity Purification and sequencing (DAP-seq), and demonstrated the coordinated interplay between epiRE sequence contexts, epigenetic factors, and transcription factors in regulating subgenome divergent transcriptional responses to external changes. Thus, this study provides a wealth of resources for elucidating the epiRE regulomics and subgenome-divergent regulation in hexaploid wheat, and gives new clues for interpreting genetic and epigenetic interplay in regulating the benefits of polyploid wheat.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE139019 | GEO | 2021/02/04

REPOSITORIES: GEO

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Project description:Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research.

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An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses

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