NOT the Brazilian aardvark

The white-nosed coati Nasua narica is a member of the raccoon family. They are native to North, Central and South America, from Arizona to Argentina. Males and females look alike, but males are much larger. As a result, for a while biologists thought solitary male coatis were a separate species from the females! [1]

Today, we share a $1K short-read genome assembly for Pearl, the white-nosed coati from the Houston Zoo. That’s her on the cover image! We thank Houston Zoo/Stephanie Adams for the cover photo.

Read more about the assembly strategy employed here in (Dudchenko et al., 2018).

This is the third member of the raccoon family (Procyonidae) we’ve assembled at DNA Zoo, making genomic analysis of raccoon-family karyotypes possible for the first time. See below how the new genome assembly for the coati compares to those of the common raccoon (Procyon lotor) and the kinkajou (Potos flavus). We see a highly conserved karyotype across all three species.

Whole-genome alignment plots between the white-nosed coati genome assembly (Nasua_narica_HiC) and the assemblies for the kinkajou (Potos_flavus_HiC) and the common raccoon (pl-1k). All species have a chromosome count of 2n=38.

In fact, the karyotype is so conserved that you can easily trace it all the way across the Carnivora order, some 40M years to the common ancestor! See below, for example, how the genome of the white-nosed coati (2n=38) compares to that of the house cat (Felis catus, genome assembly by Pontius et al., 2007), with only a few interchromosomal rearrangements. One supposes this at least to some degree justifies the early settlers mistaking Maine Coons for hybrids between raccoons and cats… Not all that surprising, but not as much genomic conservation when coati’s are compared to aardvarks, also shown below. So, if you are one of those using the term “Brazilian aardvark” to refer to coatis, look at the whole genome alignment plot, think again and read this New Yorker article! :)

Whole-genome alignment between the white-nosed coati genome (Nasua_narica_HiC) and the house cat genome (felCat8). Also show is the whole-genome alignment plot between the coati and the aardvark, genome assembly by the DNA Zoo (OryAfe1.0_HiC).

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.

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!