Potato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day-dependent tuber development. Herein, we present a high-quality, chromosome-scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein-coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome-wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.

中文翻译：

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同源四倍体马铃薯基因组提供了对高度杂合物种的见解

马铃薯 ( Solanum tuberosum L.) 起源于安第斯山脉，通过短日依赖的块茎发育演变出其无性繁殖策略。在这里，我们提出了一个四倍体马铃薯品种的高质量、染色体​​尺度的参考基因组序列。该基因组组装的总长度为 2.67 Gb，支架 N50 和 contig N50 大小分别为 46.24 和 2.19 Mb。总共通过从头获得了 1.69 Gb 的重复序列注释和长末端重复是主要的转座因子。共注释了126 070个蛋白质编码基因，其中125 077个（99.21%）位于染色体上。48条染色体被分为四种单倍型。我们注释了 31 506 个同源基因，其中 5913 个（18.77%）基因有四个同源物，11 103 个（35.24%）有三个同源物，12 177 个（38.65%）有两个同源物，2313 个（7.34%）有一个同源物。MLH3、MSH6/7和RFC3与二倍体马铃薯基因组相比，与错配修复途径相关的基因在四倍体马铃薯基因组中显着扩增。全基因组关联分析表明，150个四倍体马铃薯的细胞色素P450、类黄酮合成、查尔酮酶、糖基水解酶和糖基转移酶基因与马铃薯块茎的肉色显着相关。这项研究为高度杂合的同源四倍体马铃薯基因组提供了有价值的见解，并可能促进马铃薯品种育种工具的开发和对同源四倍体作物的进一步研究。