Populus deltoides has important ecological and economic values, widely used in poplar breeding programs due to its superior characteristics such as rapid growth and resistance to disease. Although the genome sequence of P. deltoides WV94 is available, the assembly is fragmented. Here, we reported an improved chromosome-level assembly of the P. deltoides cultivar I-69 by combining Nanopore sequencing and chromosome conformation capture (Hi-C) technologies. The assembly was 429.3 Mb in size and contained 657 contigs with a contig N50 length of 2.62 Mb. Hi-C scaffolding of the contigs generated 19 chromosome-level sequences, which covered 97.4% (418 Mb) of the total assembly size. Moreover, repetitive sequences annotation showed that 39.28% of the P. deltoides genome was composed of interspersed elements, including retroelements (23.66%), DNA transposons (6.83%), and unclassified elements (8.79%). We also identified a total of 44 362 protein-coding genes in the current P. deltoides assembly. Compared with the previous genome assembly of P. deltoides WV94, the current assembly had some significantly improved qualities: the contig N50 increased 3.5-fold and the proportion of gaps decreased from 3.2% to 0.08%. This high-quality, well-annotated genome assembly provides a reliable genomic resource for identifying genome variants among individuals, mining candidate genes that control growth and wood quality traits, and facilitating further application of genomics-assisted breeding in populations related to P. deltoides.

中文翻译：

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基于纳米孔测序和 Hi-C 技术的杨柳科植物三角杨 (Eastern Cottonwood) I-69 基因组组装

三角杨具有重要的生态和经济价值，因其生长快、抗病性强等优良特性，被广泛用于杨树育种项目。虽然 P. deltoides WV94 的基因组序列可用，但组装是零散的。在这里，我们通过结合纳米孔测序和染色体构象捕获 (Hi-C) 技术报告了 P. deltoides 品种 I-69 的改进染色体水平组装。该程序集大小为 429.3 Mb，包含 657 个重叠群，其中重叠群 N50 长度为 2.62 Mb。重叠群的 Hi-C 脚手架生成了 19 个染色体级序列，覆盖了总装配大小的 97.4% (418 Mb)。此外，重复序列注释显示 39.28% 的 P. deltoides 基因组由散布元素组成，包括逆转录元素（23.66%），DNA 转座子 (6.83%) 和未分类元件 (8.79%)。我们还在当前的 P. deltoides 组装中鉴定了总共 44 362 个蛋白质编码基因。与之前的P. deltoides WV94 基因组组装相比，本次组装有一些显着的改进：contig N50 增加了3.5 倍，gap 比例从3.2% 降低到0.08%。这种高质量、注释良好的基因组组装提供了可靠的基因组资源，用于识别个体间的基因组变异、挖掘控制生长和木材品质性状的候选基因，以及促进基因组学辅助育种在与 P. deltoides 相关的种群中的进一步应用。与之前的P. deltoides WV94 基因组组装相比，本次组装有一些显着的改进：contig N50 增加了3.5 倍，gap 比例从3.2% 降低到0.08%。这种高质量、注释良好的基因组组装提供了可靠的基因组资源，用于识别个体间的基因组变异、挖掘控制生长和木材品质性状的候选基因，以及促进基因组学辅助育种在与 P. deltoides 相关的种群中的进一步应用。与之前的P. deltoides WV94 基因组组装相比，本次组装有一些显着的改进：contig N50 增加了3.5 倍，gap 比例从3.2% 降低到0.08%。这种高质量、注释良好的基因组组装提供了可靠的基因组资源，用于识别个体间的基因组变异、挖掘控制生长和木材品质性状的候选基因，以及促进基因组学辅助育种在与 P. deltoides 相关的种群中的进一步应用。