Dataset Information

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

ABSTRACT: Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

SUBMITTER: Luo MC

PROVIDER: S-EPMC7416625 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo Ming-Cheng MC Gu Yong Q YQ Puiu Daniela D Wang Hao H Twardziok Sven O SO Deal Karin R KR Huo Naxin N Zhu Tingting T Wang Le L Wang Yi Y McGuire Patrick E PE Liu Shuyang S Long Hai H Ramasamy Ramesh K RK Rodriguez Juan C JC Van Sonny L SL Yuan Luxia L Wang Zhenzhong Z Xia Zhiqiang Z Xiao Lichan L Anderson Olin D OD Ouyang Shuhong S Liang Yong Y Zimin Aleksey V AV Pertea Geo G Qi Peng P Bennetzen Jeffrey L JL Dai Xiongtao X Dawson Matthew W MW Müller Hans-Georg HG Kugler Karl K Rivarola-Duarte Lorena L Spannagl Manuel M Mayer Klaus F X KFX Lu Fu-Hao FH Bevan Michael W MW Leroy Philippe P Li Pingchuan P You Frank M FM Sun Qixin Q Liu Zhiyong Z Lyons Eric E Wicker Thomas T Salzberg Steven L SL Devos Katrien M KM Dvořák Jan J

Nature 20171115 7681

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-qualit ...[more]

PMID: 29143815

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Project description:As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant wheat varieties.

Dataset Information

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Publications

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

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