No laughing matter

The spotted hyena (Crocuta crocuta) aka the laughing hyena is a hyena species native to Sub-Saharan Africa. It is, in fact, the most common large carnivore in Africa [1].

Spotted hyenas are very unusual animals, and there are a lot of mind-blowing facts associated with the species. Unusually for a mammal, the female spotted hyena is considerably larger than the male [1]. Spotted hyenas live in large matriarchal communities. (Cinemaphiles may recall that the spotted hyenas in the film ‘The Lion King’ are led by a female named Shenzi.) Their societies are extremely complex and bear close resemblance to those of baboons and macaques [2]. Evolutionary anthropologists demonstrated that spotted hyenas outperform chimps in at least some cooperative problem-solving tests [3]. Spotted hyenas also have a very unusual reproductive anatomy, making both mating and giving birth extremely difficult. Despite this, their cubs are the largest carnivoran young relative to their mothers' weight [1].

To help understand the biology and evolutionary history of this unique animal, today we release the chromosome-length genome assembly for the spotted hyena, here. The assembly was done following the $1K-model, see (Dudchenko et al., 2018) for details. Samples from two different animals were used for this genome assembly, with both samples donated to us by SeaWorld.

Hyenas belong to the Feliformia suborder (cat relatives), and are cousins to mongooses. See below how the genome of the spotted hyena compares to that of the meerkat (a mongoose in the DNA Zoo collection) and the domestic cat (from Pontius et al., 2007) genome assemblies.

It is interesting to note that while meerkats are more closely related to hyenas (30 MY to common ancestor) than to cats (40 MY to common ancestor), karyotypically they seem to resemble cats much more than they do hyenas (compare the whole-genome alignments between the meerkat and the hyena and the meerkat and the cat, also shown below). We will know more about the evolution of the hyena karyotype once we have a chance to assemble other hyena species, so if you have access to any relevant samples, please reach out!

Whole-genome alignments between the chromosome-length genomes of the spotted hyena (Crocuta_crocuta_HiC), the meerkat (meerkat_22Aug2017_6uvM2_HiC, from DNA Zoo collection) and the domestic cat (Felis_catus_9.0, Pontius et al., 2007)

Whole-genome alignments between the meerkat (meerkat_22Aug2017_6uvM2_HiC) and domestic cat (Felis_catus_9.0). Notice how this plot looks ‘cleaner’ than the one above for the whole-genome alignment between the meerkat and the hyena, indicating a higher degree of conservation at the karyotype level.

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.