Jumping the hoops for the sable antelope

The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is a species that is being actively managed in ranches and zoos all over the United States. To help characterize the genetic status of the managed population as compared to the wild, our colleagues from the Smithsonian Conservation Biology Institute Klaus-Peter Koepfli and Budhan Pukazhhenthhi with coauthors have recently created a draft genome assembly for the sable antelope, now available through G3: Early Online web page.

Today we share a chromosome-length assembly based on this draft, with a sample for the Hi-C library preparation provided to us by SeaWorld.

Check out below how the 30 chromosomes of the new assembly relate to the 30 chromosomes of the cow Bos taurus (genome assembly Bos_taurus_UMD_3.1.1, from Zimin et al., Genome Biology, 2009). The results suggest extensive homology!

Whole-genome alignment plot between the chromosomes in the new sable antelope genome assembly (Sable_antelope_Masurca.scf_HiC) and those of the domestic cow (Bos_taurus_UMD_3.1.1, from Zimin et al., 2009).

Less worry, more cassowary

We continue our exploration of flightless bird genomics with a chromosome-length upgrade to a southern cassowary genome assembly, also based on work from (Sackton et al., Science, 2019).

Southern cassowary is one of the three living species of cassowary, and is related to emus and rheas; see the relevant emu and rhea blog posts!

Thank you Houston Zoo for the sample used to prepare the Hi-C library!

Explore below the whole genome alignment plots for the new assembly. The results confirm our previous observation for extensive conservation of synteny between autosomes, observed all the way to chicken (100MY to common ancestor), but not so much for the sex chromosome (#5 for cassowary, #34 for the chicken genome assembly).

Whole-genome alignments between the new chromosome-length genome assembly of the southern cassowary, the emu and the chicken genome assembly (GRCg6a).

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).