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.

Bases for everyone

Today, we are happy to announce the public release of raw sequencing data to catch up with the 100 shared genome assemblies on NCBI Sequence Read Archive.

As previously, the data is shared under BioProject accession PRJNA512907. The new submission covers raw Hi-C data for 33 species and raw WGS data for 7 species. In total, the DNA Zoo BioProject data now spans 190 experiments and 11,118,071,473,442 bases!

We thank Illumina, Macrogen, Novogen, the Broad Institute and Baylor College of Medicine GARP core for their help with the data production!

As always, we share the data without restrictions: see our data usage policy here.

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Celebrating 100 assemblies

Today, we are excited to hit the 100 assemblies mark on the DNA Zoo website with the release of 4 new mammalian genome assemblies: for the German Shepherd Dog (Canis lupus familiaris, German Shepherd Dog breed), here, the Eurasian otter (Lutra lutra), here, the coppery ringtail possum (Pseudochirops cupreus), here, and the golden ringtail possum aka plush-coated ringtail possum (Pseudochirops corinnae), here.

The German Shepherd Dog (GSD) is one of the most common breeds on earth. German Shepherds are known for their intelligence and strength, but are afflicted with a range of genetic diseases. To aid with the future disease and evolutionary studies, we have created a GSD genome assembly as part of a collaborative effort led by J. William O. Ballard at the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia. The full list of people who contributed to building the resource includes: Matt A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva K.F. Chan, Andre E. Minoche, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Richard J. Edwards, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanovic, Martin Smith, Erez Lieberman Aiden, Timothy P.L. Smith, Robert A. Zammit and J. William O. Ballard. The genome assembly is now available on NCBI at https://www.ncbi.nlm.nih.gov/nuccore/VSDE00000000.1/.

The Eurasian otter is a ‘Near Threatened’ species from the IUCN Red List. It is a keystone species in the UK, which is why the Wellcome Sanger Institute made assembling the genome for this species a priority as part of its 25 Genomes Project. In collaboration with Sanger, today we release the chromosome-length assembly for the Eurasian otter, here. The fasta sequence is also available through the Vertebrate Genomes Portal, here.

Finally, in collaboration with the Mallarino Lab at Princeton University we share chromosome-length genome assemblies for two more marsupials: the coppery ringtail and the golden ringtail. We are grateful to the Australian Biological Tissue Collection at the South Australian Museum that donated material used for generating the sequencing libraries for these genome assemblies. Included in the share are the homology-based annotations for the species, courtesy MacManes Lab.

We are grateful to Terry Reis (https://www.reisecology.com) for giving us permission to use his photo for the coppery ringtail possum. We were not as lucky with the golden ringtail possum, so if you guys have any photos that you would like to donate, don’t hesitate to reach out!