Summary
The 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.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.12860

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

Some of the World's most valuable crops, including watermelon, honey melon, cucumber, squash, zucchini and pumpkin, belong to the family Cucurbitaceae. We review insights on their domestication from new phylogenies, archaeology and genomic studies. Ancestral state estimation on the most complete Cucurbitaceae phylogeny to date suggests that an annual life cycle may have contributed to domestication. Domestication started c. 11 000 years ago in the New World and Asia, and apparently more recently in Africa. Some cucurbit crops were domesticated only once, others multiple times (e.g. melon from different Asian and African populations). Most wild cucurbit fruits are bitter and nonpalatable to humans, and nonbitterness of the pulp apparently was a trait favoured early during domestication, with genomic data showing how bitterness loss was achieved convergently. The genetic pathways underlying lycopene accumulation, red or orange pulp colour, and fruit size and shape are only just beginning to be understood. The study of cucurbit domestication in recent years has benefitted from the increasing integration of archaeological and genomic data with insights from herbarium collections, the most efficient way to understand species' natural geographic ranges and climate adaptations.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16015

Origin and domestication of Cucurbitaceae crops: insights from phylogenies, genomics and archaeology

Striking increases in fruit size distinguish cultivated descendants from small-fruited wild progenitors for fleshy fruited species such as Solanum lycopersicum (tomato) and Prunus spp. (peach, cherry, plum, and apricot). The first fruit weight gene identified as a result of domestication and selection was the tomato FW2.2 gene. Members of the FW2.2 gene family in corn (Zea mays) have been named CNR (Cell Number Regulator) and two of them exert their effect on organ size by modulating cell number. Due to the critical roles of FW2.2/CNR genes in regulating cell number and organ size, this family provides an excellent source of candidates for fruit size genes in other domesticated species, such as those found in the Prunus genus. A total of 23 FW2.2/CNR family members were identified in the peach genome, spanning the eight Prunus chromosomes. Two of these CNRs were located within confidence intervals of major quantitative trait loci (QTL) previously discovered on linkage groups 2 and 6 in sweet cherry (Prunus avium), named PavCNR12 and PavCNR20, respectively. An analysis of haplotype, sequence, segregation and association with fruit size strongly supports a role of PavCNR12 in the sweet cherry linkage group 2 fruit size QTL, and this QTL is also likely present in sour cherry (P. cerasus). The finding that the increase in fleshy fruit size in both tomato and cherry associated with domestication may be due to changes in members of a common ancestral gene family supports the notion that similar phenotypic changes exhibited by independently domesticated taxa may have a common genetic basis.

/pdf/cell-number-regulator-genes-in-prunus-provide-candidate-3dqxws4iqv.pdf

Cell number regulator genes in Prunus provide candidate genes for the control of fruit size in sweet and sour cherry

Cucurbita pepo is extremely diverse in fruit characteristics. Native to semi-arid and temperate regions of North America, C. pepo was domesticated at least twice, in Mexico over 10,000 years ago and in the United States over 4000 years ago. There is no evidence for the existence of Cucurbita in the Old World prior to 1492. Pumpkins and squash of C. pepo are today found in countries on all continents. Pumpkins are valued for their fruit flesh and seeds, as well as for ornament. Squash, especially zucchini, are an increasingly popular, short-season, high-value crop. Plant resource allocation is fundamentally different for plants on which fruits are allowed to mature, the pumpkins and winter squash, as compared with those on which the fruits are continually removed when young, the summer squash. C. pepo contains a wealth of genetic variation that could be further exploited to enhance the fruit-flesh quality of pumpkins and the flavor of summer squash. Genomic tools can be expected to aid in this effort and, especially, facilitate the introgression of disease resistance from other species of Cucurbita. Fruit quality and flavor enhancements of pumpkins and squash have been and are being accomplished largely by the consumer-oriented breeders at research and academic institutions. However, lack of support for these breeding programs is jeopardizing the continued consumer-oriented fruit-quality enhancement of C. pepo germplasm.

Germplasm enhancement of Cucurbita pepo (pumpkin, squash, gourd: Cucurbitaceae): progress and challenges

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.

https://www.biorxiv.org/content/biorxiv/early/2017/06/09/147702.full.pdf

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

Parallel Evolution under Domestication and Phenotypic Differentiation of the Cultivated Subspecies ofCucurbita pepo(Cucurbitaceae). Cucurbita pepo (pumpkin, squash, gourd, Cucurbitaceae) is an ancient North American domesticate of considerable economic importance. Based on molecular genetic polymorphisms, two cultivated lineages of this species, each consisting of very many edible–fruited cultigens, have been recognized, C. pepo subsp. pepo and C. pepo subsp. texana. However, the phenotypic commonalities and differences between these two subspecies have not as yet been systematically collected and organized. Among the evolutionary developments common to the two subspecies are the increased size of the plant parts, less plant branching, and premature loss of chlorophyll in the exocarp of the fruits. In both subspecies, bush growth habit, conferred by allele Bu, is common to the cultigens grown for consumption of the immature fruits, as is the deviation from the 1:1 ratio of fruit length to fruit width. A major characteristic differentiating between the edible–fruited cultigens of the respective subspecies are the longitudinal protrusions, in subsp. pepo, versus depressions, in subsp. texana, of the fruit surface corresponding with the subsurface primary carpellary vein tracts. Subsp. pepo also has larger fruits and larger and longer seeds. In addition, some alleles affecting stem color, leaf mottling, multiple flower bud production, and fruit characteristics are frequently occurring to nearly fixed in one subspecies but are rare to less common in the other.

Thomas C. Andres

Papers

Parallel Evolution Under Domestication and Phenotypic Differentiation of the Cultivated Subspecies of Cucurbita pepo (Cucurbitaceae)