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

Zhou, Ran; Jenkins, Jerry W.; Zeng, Yibing; Shu, Shengqiang; Jang, Hosung; Harding, Scott A.; Williams, Melissa; Plott, Christopher; Barry, Kerrie W.; Koriabine, Maxim; Amirebrahimi, Mojgan; Talag, Jayson; Rajasekar, Shanmugam; Grimwood, Jane; Schmitz, Robert J.; Dawe, R. Kelly; Schmutz, Jeremy; Tsai, Chung‐Jui

doi:10.1111/tpj.16454

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

Journal Article · 07 September 2023 · The Plant Journal

DOI: https://doi.org/10.1111/tpj.16454 · OSTI ID:1998982

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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
HudsonAlpha Institute of Biotechnology Huntsville Alabama USA
Department of Genetics University of Georgia Athens Georgia USA
DOE Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley California 94720 USA
Arizona Genomics Institute, School of Plant Sciences University of Arizona Tucson Arizona USA
Department of Genetics University of Georgia Athens Georgia USA, Department of Plant Biology University of Georgia Athens Georgia USA
HudsonAlpha Institute of Biotechnology Huntsville Alabama USA, DOE Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley California 94720 USA

SUMMARY 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.

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Sponsoring Organization:: USDOE

OSTI ID:: 1998982

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Vol. 116 Journal Issue: 4; ISSN 0960-7412

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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