School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA.
Department of Genetics, University of Georgia, Athens, Georgia, USA.
Plant J. 2023 Nov;116(4):1003-1017. doi: 10.1111/tpj.16454. Epub 2023 Sep 7.
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.
杨属物种在多样化的生态系统中发挥着基础作用，是生物能源和生物制品的重要可再生原料。杂种欧洲山杨（Populus tremula × P. alba INRA 717-1B4）是树木功能基因组学和生物技术研究中广泛使用的转化模型。作为一种异花授粉的种间杂种，其基因组中存在大量序列多态性，这给序列敏感分析带来了挑战。在这里，我们报道了该杂种欧洲山杨的端粒到端粒基因组，该基因组由两个染色体尺度、单倍型分辨率的组装组成。我们对重复序列景观进行了全面分析，并鉴定了串联重复序列和无重复序列的着丝粒。出乎意料的是，两个单倍型中最丰富的卫星重复序列位于着丝粒之外，由一个 147bp 的单体 PtaM147 组成，经常跨越>1 兆碱基，并形成异染色质结。PtaM147 重复序列仅在杨属（柳属）植物中检测到，但在亲缘关系密切的物种的 LTR-逆转录转座子中存在 PtaM147 样序列，这表明它们起源于逆转录转座子。为该转化模型基因型生成的基因组资源极大地改进了对序列多态性高度敏感的基因组编辑实验的设计和分析。这项工作应该会激发未来的假设驱动研究，以探究丰富的、仅存在于杨属植物中的 PtaM147 卫星 DNA 的功能。
