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Pumpkin patch

Cucurbita (Latin for gourd) is a genus of herbaceous plants. Five species are grown worldwide for their edible plants that we all know as pumpkins and squashes. Cucurbits are native to Andes and Mesoamerica, and are one of the oldest of domesticated plants. The earliest known evidence of the domestication of Cucurbita dates back at least 8,000 years ago, predating the domestication of other crops in the area such as maize and beans by some 4000 years! [1]

Today we are releasing chromosome-length genome upgrades for three of the cultivated cucurbit species: Cucurbita pepo (pumpkin, zucchini, yellow summer squash, acorn, vegetable marrow, many ornamental gourds etc.), Cucurbita moschata (butternut squash, calabaza, crookneck etc.) and Cucurbita maxima (buttercup squash, Boston marrow, kabocha etc.). The upgrades are based on two papers: (Sun, Wu et al., Mol. Plant 2017) for C. moschata and C. maxima and (Montero-Pau, Blanca et al., Plant Biotechnol. 2018) for C. pepo. For C. pepo we polished pseudomolecules put together using linkage data.

As usual, the upgrades involved some Hi-C experiments. In this case, the material for the upgrades was obtained from Pinetree Garden Seeds, the experiments performed by Melanie Pham (DNA Zoo). Heirlooms used were Black Futsu squash (C. moschata), Trivoli spaghetti squash (C. pepo) and Galeux d'Eysines squash (C. maxima).

See whole-genome alignments below to learn how the genomes of various pumpkins relate to each other. The results suggest that C. pepo and C. moschata have very similar karyotypes, but C. maxima has an inversion in one of the chromosomes (#4 in C. pepo/#16 in C. maxima).

Whole-genome alignment plots for new genome assemblies: C. pepo (ASM280686v2_HiC), C. moschata (Cmos_1.0_HiC) and C. maxima (Cmax_1.0_HiC).

Also note the secondary diagonal stretches in the plots above. E.g. the p-arm of chr17 in C. moschata aligns well not only to p-arm of chr2 of C. pepo but also to p-arm of chr6. Similarly, p-arm of chr8 in C. pepo aligns not only to chr13, but also to chr10 in P. moschata. These sequence similarities are a reflection of an ancient allotetraploidization event likely involving hybridization between two highly diverged diploid progenitors. The duplication is even more obvious when comparing the genome assemblies of gourds with more distant relatives without the duplication such as cucumber, below. Read more about this also in (Sun, Wu et al., Mol. Plant 2017) and (Montero-Pau, Blanca et al., Plant Biotechnol. 2018).

Whole-genome alignment between the cucumber genome assembly (ASM407v2, from Ren, Zhang, Liu et al., 2009) and the updated C. pepo genome assembly (ASM280686v2_HiC).

Cover image credit: Roots ‘n’ Shoots blog. We thank Zane Colaric (DNA Zoo) for help with this blog post.

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