De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus

The Cucurbita genus 南瓜属 (squashes 笋瓜, pumpkins 南瓜 and gourds 葫芦) includes important domesticated species (驯化物种) such as C. pepo (西葫芦), C. maxima (笋瓜) and C. moschata (南瓜). In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family (葫芦科). The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits (瓜类) belonging to the Cucumis (黄瓜属) and Citrullus genera (西瓜属), and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus.

南瓜属包含许多重要的驯化物种，包括西葫芦、笋瓜和南瓜。本文对西葫芦进行了全基因组测序并得到了高质量的基因组草图。组装大小为263Mb，scaffold N50长1.8Mb，预测到34 240个基因模型。预测的西葫芦基因覆盖了BUSCO库保守的核心基因的92%，这些基因占整个基因组的93%。通过7718个SNPs构建的遗传图谱，作者将这些scaffold锚定到20个假染色体上。除了西葫芦基因组较小以外，作者通过基因家族系统树构建、核型排序及4DTv分析三条独立的分析方法得到了同样的结论，就是西葫芦基因组发生过一次全基因组复制事件。另外，作者还测序并从头组装了南瓜属12个物种40个转录组，并且与其他西葫芦科已测序的物种一起进行了分析。在所有南瓜属的物种中都检测到了全基因组复制事件，包括笋瓜和南瓜，但在其他的瓜类如黄瓜属和西瓜属中就没有检测到全基因组复制事件，综合来看，南瓜属鉴定到的全基因组复制事件大概发生于30个百万年左右。

doi: 10.1111/pbi.12860