The scimitar oryx strikes back

The scimitar-horned oryx (Oryx dammah) is a member of the subfamily Hippotraginae (the “horse antelopes”), one of the subfamilies included in the ruminant family Bovidae (which includes the domestic varieties of cows, goats, and sheep). The assembly of the sable antelope, another member of this subfamily, was previously published by the DNA Zoo. The scimitar-horned oryx may be the source of the unicorn myth in antiquity!

At one time, scimitar-horned oryx migrated widely across the grassy steppes of the Sahel and edges of the Sahara Desert in north Africa. This species displays adaptive hyperthermia, as animals can tolerate internal temperatures of 116ºF, which helps them to conserve water in their desert environment. Due to over-hunting and habitat loss, the species was declared “Extinct in the Wild” in 2000 by the IUCN Red List of Threatened Species, a designation that remains to this day.

However, through successful global captive breeding and management efforts, and led by the Environment Agency of Abu Dhabi and the Sahara Conservation Fund, scimitar-horned oryx were reintroduced back into the wild in Chad in 2016, with additional individuals returned in 2017 and 2018. Calves have been born and the population is slowly growing, with the hope that there will be large enough numbers of scimitar-horned oryx so that they become independent of human care. You can learn more about The Scimitar-horned Oryx Reintroduction Program in Chad at the Sahara Conservation Fund website.

Today, we share the chromosome-length assembly for the scimitar-horned oryx. The draft assembly for this release was generated using 10x Genomics linked-read sequencing and Supernova version 2.0 using genetic material from a male individual from the captive herd at the National Zoological Park – Conservation Biology Institute in Front Royal, Virginia, USA. The Hi-C upgrade was based on a female sample from the same herd. We hope the new chromosome-length assembly will serve as a foundation for genomic research aimed at the conservation of both captive and reintroduced populations of this iconic antelope species. Find out more about the assembly and its use in our recent preprint (Humble et al., 2019)!

You won't believe these cat pix - #1 is a total blast!!!

Cacomistle (Bassariscus sumichrasti) is a nocturnal animal native to Central America, with its habitat spanning from Southern Mexico to Panama [1]. The name cacomistle comes from the Nahuatl language meaning “half-cat” [2], but don't be fooled by the name! Cacomistles aren’t related to cats. In fact, the black ringed tail of the cacomistle hints on its family resemblance to the common racoon, a species we’ve recently assembled at the DNA Zoo alongside the white-nosed coati and kinkajou in the same family.

Today, we share a chromosome length assembly for a cacomistle using a fibroblast cell line provided to us by the T.C. Hsu CryoZoo at the University of Texas MD Anderson Cancer Center. These were originally frozen all the way back in the summer of 1976! Fast-forward 45 years, and the cells feel great: pictured below is the confluent cell line after just 6 days of culturing. We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with the samples!

This is a $1K genome assembly with contig N50 = 45kb and scaffold N50 = 125Mb. See Dudchenko et al., 2018 for details on the procedure!

44 year old cacomistle fibroblasts from the T.C. Hsu CryoZoo at MD Anderson Cancer Center.

Moves like jaguar

The jaguar (Panthera onca) is a large felid species, and the only remaining member of the Panthera genus native to the Americas [1]. These amazing animals have the most powerful bite of all big cats, and are aptly named. The word ‘jaguar’ comes from the Tupian word ‘yaguara’ which means ‘beast of prey’. The jaguar is listed as near threatened on the ICUN’s red list due to loss of habitat [2]. Read more about the jaguar on panthera.org website and learn about the Jaguar Corridor Initiative to preserve the genetic integrity and future of the jaguar by connecting and protecting core jaguar populations from Mexico to Argentina!

Today, we share the chromosome-length assembly for the jaguar named Cocoy from the Houston Zoo. Sadly, Cocoy passed away in 2015, but her genome lives on in the digital form and will hopefully help the jaguar species in the years to come. This is a $1K genome assembly, see Dudchenko et al., 2018 for strategy details.

This is the sixth felid assembly in our collection alongside the cheetah, leopard, tiger, cougar, and clouded leopard. As pointed out before (see, e.g. this blog post) the Felidae karyotype is very highly conserved, confirmed once again in the whole-genome alignment plot between the domestic cat genome assembly, from Pontius et al., Genome Res., 2007, and the new jaguar genome assembly.

Whole genome alignment between the new jaguar genome assembly (Panthera_onca_HiC) and the domestic cat genome assembly (felCat9, NCBI accession number GCF_000181335.3).