Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.

栽培马铃薯（Solanum tuberosum L.）是一类高度杂合的同源四倍体（autotetraploid），其基因组分析与育种工作均面临诸多挑战。野生马铃薯物种是将重要农艺性状渐渗（introgression）至栽培马铃薯的宝贵种质资源。其中关键物种之一为查科马铃薯（Solanum chacoense）及其二倍体自交克隆M6，该克隆具备自交亲和性，同时拥有优良的块茎商品品质与抗病性状。研究团队对查科马铃薯M6克隆的基因组开展测序与组装，最终获得总长825,767,562 bp的基因组序列，共包含8260个支架序列（scaffold），其N50支架序列长度为713,602 bp。通过伪分子（Pseudomolecule）构建，将508 Mb的基因组组装序列锚定至12条染色体。基因组注释共得到49,124个高可信度基因模型，对应37,740个功能基因。将M6基因组与另外6个茄科（Solanaceae）物种进行比较分析，鉴定得到158,367个茄科核心基因，以及仅存在于3个马铃薯物种中的1,897个特异基因。对M6全基因组的单核苷酸多态性（single nucleotide polymorphism, SNP）分析显示，相较于其余染色体，第4、8、9号染色体呈现出更高水平的残留杂合性。获取M6基因组序列，可为重要农艺性状关键基因的挖掘提供重要资源，同时有助于推动基于基因组学的二倍体自交马铃薯培育工作，进而有望加速马铃薯育种进程。