SEAL Team

Harbor seals are one of the most common marine mammals. The global population of harbor seals is 350,000–500,000, but subspecies in certain habitats are threatened [1]. Once a common practice, sealing is now illegal in many nations within the animal's range, and in the US harbor seals, like all marine mammals, are protected under the Marine Mammal Protection Act.

To contribute to the work done on harbor seal conservation and management we share the chromosome-length assembly, here. This work is based on the draft genome assembly generated by the Canada's Genome Enterprise (CGEN). We thank SeaWorld for the sample used for Hi-C library preparation!

See below how the chromosomes of the new genome assembly compare to another pinniped recently assembled by the DNA Zoo, the Northern elephant seal (Mirounga angustirostris). The karyotypes appear to be practically identical up to a chromosome fusion event: chromosomes #9 and #2 in the Northern elephant seal = chromosome #2 in the harbor seal assembly.

Whole genome alignment plot between the genome assemblies of the harbor seal (GSC_HSeal_1.0_HiC) and the Northern elephant seal (Mirounga_angustirostris_HiC).

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).