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

Abstract

SummaryThe Cucurbita genus (squashes, pumpkins and 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 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. The duplication was detected in all the Cucurbita species analysed, 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 occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus.

The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita

“…We assembled the C. argyrosperma nuclear genome into 920 scaffolds (1481 contigs), with an N 50 of 620 880 bp (Table 1). The total length of the assembled scaffolds was $229 Mbp, around 96% of the estimated size of the genome and similar to the assembly size of previously reported Cucurbita genomes (Montero-Pau et al, 2017;Sun et al, 2017). Genome completeness was assessed by finding single-copy orthologous genes conserved in embryophytes (1440) using BUSCO (Simã o et al, 2015).…”

“…Even though the genomic footprints of a whole-genome duplication are strong in Cucurbita, the numbers of predicted proteincoding genes in Cucurbita genomes are roughly similar to those in other genomes of the Cucurbitaceae family (Huang et al, 2009;Garcia-Mas et al, 2012;Guo et al, 2012;Montero-Pau et al, 2017;Sun et al, 2017;Urasaki et al, 2017;Wu et al, 2017). This apparent lack of duplicated coding genes could be the result of ''pseudogenization'' processes, implying a loss of redundant genes throughout the evolution of the Cucurbita genomes, either by the accumulation of mutations resulting in loss of function or fractionation due to intrachromosomal recombination .…”

“…Recent advances in the study of Cucurbita spp. genomes revealed a recent whole-genome duplication around 30 million years ago (Mya) in the common ancestor of the genus (Montero-Pau et al, 2017;Sun et al, 2017).…”

An integrated transcriptomics and metabolomics analysis of the Cucurbita pepo nectary implicates key modules of primary metabolism involved in nectar synthesis and secretion

“…Over 240M reads (50 bp, paired end) derived from squash nectary RNAs were assembled into 70,111 contigs and initially mapped to both the C. melo (melon) and Arabidopsis thaliana Col‐0 genomes, with the corresponding C. pepo orthologs [from the recently published zucchini genome (Montero‐Pau et al., )] to the C. melo genes subsequently being incorporated into the analysis. The rationale for mapping contigs to melon is that it is a close relative to squash with a fully sequenced genome; similarly, contigs were mapped to Arabidopsis because it has a very well annotated genome and has served as the genetic model for plant biology, including the process of nectar production [reviewed in (Roy et al., )].…”

Long‐read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

“…Knowledge of genetic variation is a prerequisite for effective utilization in crop breeding, biological research and relationship analyses among species (Prakash et al, ). Although several genomes of Cucurbitaceae species have been assembled over the past decade, such as Carica papaya (Ming et al, ), Cucumis melo (Garcia‐Mas et al, ), Cucumis sativus (Huang et al, ), Citrullus lanatus (Guo et al, ), Cucurbita maxima (Sun et al, ), Cucurbita moschata (Sun et al, ) and Cucurbita pepo (Montero‐Pau et al, ), their genomes have provided only limited information regarding gene and genetic variation discoveries in Luffa species. To address these limitations, a high‐quality reference genome analysis of Luffa cultivars was performed to expand our knowledge of sponge gourd genome function and evolution.…”