Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun., using PacBio long-read sequencing, Optical mapping, and Hi-C scaffolding technologies. The final sequence assembly consisted of 737.9 Mb, among which 647.0 Mb were anchored to the 12 chromosomes. Compared with chromosome-scale assemblies of S. lycopersicum (tomato), S. etuberosum (non-tuber-bearing species with E genome), S. verrucosum, S. chacoense, S. multidissectum, and S. phureja (all four are A-genome species), the S. bulbocastnum genome was the shortest. It contained fewer transposable elements (56.2%) than A-genome species. A cluster analysis was performed based on pairwise ratios of syntenic regions among the seven chromosome-scale assemblies, showing that the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum. Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species. Therefore, the S. bulbocastanum genome differs in genome structure and gene sequences from the A-genome species. These findings provide important insights into understanding and utilizing the genetic diversity of S. bulbocastanum and the other Mexican diploid species in potato breeding.

中文翻译：

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Solanumbulbocastanum Dun. 的从头基因组组装，这是一种从 A 基因组物种（包括栽培马铃薯）中生殖分离的墨西哥二倍体物种

马铃薯及其野生近缘种主要分布在墨西哥高地和南美洲安第斯山脉中部。南美 A 基因组物种，包括栽培马铃薯，与墨西哥二倍体物种生殖分离。全基因组测序揭示了基因组结构和相似性，主要是在栽培马铃薯及其密切相关的物种中。在这项研究中，我们使用 PacBio 长读长测序、光学图谱和 Hi-C 支架技术，对墨西哥二倍体物种 Solanum tubecastanum Dun. 的基因组进行了染色体规模的组装。最终的序列组装由 737.9 Mb 组成，其中 647.0 Mb 锚定在 12 条染色体上。与 S. lycopersicum（番茄）、S. etuberosum（具有 E 基因组的非块茎物种）、S. verrucosum、S. chacoense、S. multidissectum 和 S. phureja（所有四种都是 A -基因组物种），S. tuberbocastnum 基因组是最短的。它含有比 A 基因组物种更少的转座元件 (56.2%)。根据七个染色体规模组件中同线性区域的成对比率进行聚类分析，表明 A 基因组物种首先被聚类为一个不同的群体。然后，该群体与 S.bulbocastanum 聚集在一起。 36 个茄属物种和克隆中 1,624 个单拷贝直系同源基因组的序列相似性将 S.bulbocastanum 作为一个特定组（包括其他墨西哥二倍体物种）与 A 基因组物种分开。因此，S.bulbocastanum 基因组在基因组结构和基因序列方面与 A 基因组物种不同。这些发现为理解和利用马铃薯育种中的 S.bulbocastanum 和其他墨西哥二倍体物种的遗传多样性提供了重要的见解。