De-novoassembly of zucchini genome reveals a whole genome duplication associated with the origin of theCucurbitagenus

Abstract

The Cucurbita genus (squashes, pumpkins, gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata . 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, 34,240 gene models, 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 7,718 SNPs. Despite its small genome size three independent evidences 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 analyzed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analyzed, including C. maxima and C. moschata , but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have happened 30 ± 4 Mya in the ancestral species that gave rise to the genus.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes

“…We identified 195 paralogous syntenic blocks (7773 homoeologous gene pairs) in C. maxima and 170 blocks (7742 gene pairs) in C. moschata, with synonymous substitution rate (Ks) values peaking at 0.32 ( Figure 2A and Supplemental Figures 5 and 6), collectively covering 92.5% and 94.1% of the gene space, respectively. These homoeologous pairs clearly indicated that both C. maxima and C. moschata genomes underwent a wholegenome duplication (WGD) event that was also reported in another Cucurbita species, C. pepo (Montero-Pau et al, 2017), but not observed in other sequenced cucurbits, including cucumber (Huang et al, 2009), melon (Garcia-Mas et al, 2012), watermelon (Guo et al, 2013), and bitter gourd (Momordica charantia) (Urasaki et al, 2017) (Figure 2A).…”

Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

“…Compared to hundreds of shared markers in previous studies [21], much more cross-species transferable SSR markers in Cucurbita genus were used for chromosome synteny analysis in our study. It might be the case that there had a WGD event leading to the high abundance of SSR markers [8,9], but it's not observed in other sequenced Cucurbitaceae species, such as cucumber [15], melon [48], watermelon [16].…”

“…In 2012, the planting area of pumpkin in China was about 3.8×10 4 Hm 2 , and the total output reached 7.0×10 6 tons (http://faostat3.fao.org/). Cucurbita species have a relatively smaller genome sizes and a greater chromosome numbers compared with other Cucurbitaceous crops [7], and the assembled genome sizes are 271.4 Mb for C. maxima, 269.9 Mb for C. moschata, and 263 Mb for C. pepo, respectively [8,9]. With a long history of cultivation and domestication, the morphological variation of Cucurbita species shows a higher diversity in fruit shape, size and color than other Cucurbitaceae species [10].…”

Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)

“…Genomic resources and genetic transformation protocols have recently become available in Cucurbita (Montero‐Pau et al, , ; Nanasato, Okuzaki, & Tabei, ; Sun et al, ). Alongside improvements in the characterization of genetic diversity within the crop wild relatives, these resources are facilitating breeding and genetic research (e.g., Holdsworth, LaPlant, Bell, Jahn, & Mazourek, ).…”