On the Origin of Darwins

Kinkajous (Potos flavus) are tropical forest mammals related to raccoons. Just like pandas, despite being classified in the carnivores order, their diet is mainly plant-based, and just like pandas, they have a number of cool adaptations to support the arboreal lifestyle. For example, kinkajous can rotate their ankles and feet 180° and have a prehensile tail!

Today, we share a chromosome-length short read-only assembly for Darwin, the male kinkajou living at Moody Gardens. Darwin is an ambassador animal for Moody Gardens, which means he helps educate the public about his species.

Previously, we have shared the short-read, $1K assembly for the common raccoon, a first-ever assembly in the raccoon (Procyonidae) family. Check out how the species relate to each other below!

Read more about the assembly strategy for the common raccoon and the kinkajou in (Dudchenko et al., bioRxiv, 2018).

Whole-genome alignments between the 19 chromosomes of the common raccoon (pl-1k genome assembly) and the 19 chromosomes of the kinkajou (Potos_flavus_HiC genome assembly). The species appear to have very similar karyotypes except for one chromosome (#7 in the kinkajou and #14 in the common raccoon).

A genome of rhea beauty

Today, we continue exploring paleognaths genomics with a chromosome-length assembly for another flightless bird, the greater rhea Rhea americana. Greater rheas are found throughout South America where they are the largest extant bird species. Their population is currently decreasing, and rheas are now listed as Near Threatened by the IUCN [1].

Just like our emu genome release from two weeks ago, this assembly is based on a recently published work by (Sackton et al., Science, 2019). The blood sample for Hi-C library preparation was donated by Huevo, a female greater rhea from the Houston Zoo.

We compare the genomes of the two chromosome-length paleognaths, the greater rhea and the emu (~60MY to common ancestor), as well as the genome of a representative neognath, the chicken (~100MY to common ancestor), below. Note extensive conservation of synteny between autosomes, observed all the way to chicken, but not so much for the sex chromosome (#1 in rhea, #34 in chicken).

Whole-genome alignment plots between the new chromosome-length genome assemblies of the greater rhea, emu and the chicken genome assembly (GRCg6a).

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).