Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA.

Autor:	Zhou R; School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA.; Department of Genetics, University of Georgia, Athens, Georgia, USA.; Department of Plant Biology, University of Georgia, Athens, Georgia, USA., Jenkins JW; HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA., Zeng Y; Department of Genetics, University of Georgia, Athens, Georgia, USA., Shu S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA., Jang H; Department of Genetics, University of Georgia, Athens, Georgia, USA., Harding SA; School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA.; Department of Genetics, University of Georgia, Athens, Georgia, USA.; Department of Plant Biology, University of Georgia, Athens, Georgia, USA., Williams M; HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA., Plott C; HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA., Barry KW; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA., Koriabine M; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA., Amirebrahimi M; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA., Talag J; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA., Rajasekar S; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA., Grimwood J; HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA., Schmitz RJ; Department of Genetics, University of Georgia, Athens, Georgia, USA., Dawe RK; Department of Genetics, University of Georgia, Athens, Georgia, USA.; Department of Plant Biology, University of Georgia, Athens, Georgia, USA., Schmutz J; HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA.; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA., Tsai CJ; School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA.; Department of Genetics, University of Georgia, Athens, Georgia, USA.; Department of Plant Biology, University of Georgia, Athens, Georgia, USA.
Jazyk:	angličtina
Zdroj:	The Plant journal : for cell and molecular biology [Plant J] 2023 Nov; Vol. 116 (4), pp. 1003-1017. Date of Electronic Publication: 2023 Sep 07.
DOI:	10.1111/tpj.16454
Abstrakt:	Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA. (© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)
Databáze:	MEDLINE
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