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).

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!