Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X-5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

中文翻译：

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栽培马铃薯类群的结构基因组分析。


选择了十二个马铃薯种质来代表马铃薯分类学的两种主要观点。针对三个已发表的马铃薯基因组对基因组进行了测序和结构变异（拷贝数变异）分析。普通马铃薯（Solanum tuberosum L.）是一种重要的主粮作物，具有高度杂合且复杂的四倍体基因组。栽培马铃薯的其他类群包含不同的倍性水平（2X-5X），并且这些物种的基因组中常见结构变异，可能有助于驯化过程中的多样化或农艺性状。增加对基因组和基因组变异的了解将有助于探索新的农艺性状。因此，来自代表四个倍性水平的十二个马铃薯地方品种的测序数据被用来鉴定与两个当前可用的参考基因组（双单倍体马铃薯基因组和S.chacoense的二倍体近交克隆）相比的结构基因组变异。拷贝数变异分析的结果表明，在大多数基因组中，虽然缺失的数量大于重复的数量，但重复基因的数量大于删除基因的数量。 12 个马铃薯基因组中的特定区域具有高密度的 CNV 事件。此外，相对于参考基因组，生长素诱导的 SAUR 基因（涉及非生物胁迫）、抗病基因和 2-酮戊二酸/Fe(II) 依赖性加氧酶超家族蛋白等，在这些测序基因组中的拷贝数有所增加。