On pins and needles

About 40% of all mammal species are rodents (2,277 species); they are found in vast numbers on all continents except Antarctica [1]. To contribute to research on rodent evolution, today we are releasing a chromosome-length de novo assembly of a new rodent species, entirely from short reads.

The Brazilian porcupine Coendou prehensilis is a porcupine found in Brazil, Argentina, Venezuela, the Guyanas, Bolivia and Trinidad. Brazilian porcupines are well adapted to live and move in trees, with their muscular prehensile tail, hence the binomial C. prehensilis.

A blood sample for this genome assembly was donated by Bobby-Sue, a Brazilian porcupine from Moody Gardens. Thanks to the Moody Gardens team for their help!

Check out how the 37 chromosomes of the new genome align to the 20 chromosomes of the house mouse Mus musculus (genome assembly GRCm38) and the 32 chromosomes of the guinea pig Cavia porcellus, a more closely related rodent from among the DNA Zoo releases, shared here.

Whole-genome alignments between the chromosome-length genome assemblies for the Brazilian porcupine (Coendou_prehensilis_HiC), the house mouse (GRCm38, by the Genome Reference Consortium), left, and the guinea pig (Cavpor3.0_HiC, DNA Zoo upgrade from Lindblad-Toh et al., 2011).

An emuzing genome

Today, we are releasing an upgrade to the genome assembly of emu, Dromaius novaehollandiae. Emus are the second-largest living bird, by height, and the largest bird in Australia where it is endemic.

This genome assembly is based on a recently published work by (Sackton et al., Science, 2019). We thank SeaWorld for the sample used for Hi-C library preparation!

The emu genome assembly is the first Palaeognathae bird to be released by the DNA Zoo, and the first ever chromosome-length genome assembly in Paleognathae. Palaeognathae, or paleognaths, is one of the two living clades of birds – the other being Neognathae [1]. Check out how the emu chromosomes relate to those of chicken – a representative neognathan, below.

Whole-genome alignment plot between the new chromosome-length genome assembly of emu and the chicken genome assembly (GRCg6a).

Palaeognathae contains five extant branches of flightless lineages (plus two extinct clades), termed ratites, and one flying lineage, the tinamous. Read about the latest insights into molecular evolution of flightlessness in (Sackton et al., Science, 2019), and stay tuned for more!

Seal of approval

The Northern elephant seal Mirounga angustirostris nearly went extinct in the late 19th century. While the species made a dramatic recovery, with 200,000+ individuals alive today, they are all descendants of fewer than 100 individuals that found refuge on the Guadalupe Island, Mexico [1, 2].

Today, we are sharing a chromosome-length genome assembly for the Northern elephant seal (contig N50: 76 kb; scaffold N50: 140 Mb) generated entirely from short Illumina reads (PE150, see Methods for more details on the workflow). The samples for library construction have been collected at Año Nuevo State Park in California by Jane Khudyakov (University of the Pacific) and Daniel Crocker (Sonoma State University). We thank Ben Neely at NIST for coordinating the effort to collect these valuable samples!

Prior to the recent genome releases here at DNA Zoo, the only de novo chromosome-length assembly in the dog-like family (the suborder Caniformia) was the dog itself (Canis lupus familiaris), which diverged from seal ~50 million years ago. Below, you can see that the two species have very different karyotypes.

At DNA Zoo, we have now released eleven other Caniformia genomes: red panda (Ailurus fulgens), dingo (Canis lupus dingo), sea otter (Enhydra lutris), African wild dog (Lycaon pictus), domestic ferret (Mustela putorius furo), walrus (Odobenus rosmarus), common raccoon (Procyon lotor), American black bear (Ursus americanus), grizzly bear (Ursus arctos), polar bear (Ursus maritimus) and red fox (Vulpes vulpes). The most apt comparison is with walrus (Odobenus rosmarus), the only other pinniped in the DNA Zoo. The most recent common ancestor of the walrus and the seal lived ~35 million years ago. They show much stronger conservation of synteny. The data contrast helps illustrate the fact that the dog has one of the most extensively rearranged mammalian karyotypes investigated so far.

The genome assemblies for the walrus and dog used in the analysis can be found here and here, respectively.

Whole-genome alignment plots between the walrus (left) and domestic dog (right) to the Northern elephant seal genome assemblies.