No probllama

The llama (Lama glama) is a domesticated South American camelid, widely used as a meat and pack animal by Andean cultures since the Pre-Columbian era.

Today, we release the chromosome-length assembly for the llama named Fiesta, living at the Houston Zoo. Fiesta is pretty famous! Check out this viral video of her enjoying the leaf blower. This is a $1K short-read assembly.

This is the third camelid in our collection, the other two being the dromedary and the alpaca, both upgrades from previously available genomes. Check the whole-genome alignments below: looks like the camel karyotype has been very stable over the last 45MY or so!

Whole-genome alignment plots between the new genome assembly for the llama (Lama_glama_HiC) and the dromedary (PRJNA234474_Ca_dromedarius_V1.0_HiC) and alpaca (Vicugna_pacos-2.0.1_HiC) genome assemblies. All assemblies have the same diploid chromosome number of 74.

An elephantine undertaking

The Asian elephant (Elephas maximus) is the largest land mammal in Asia and the most endangered species of elephant (1). Once ranging from Iran to Southeast Asia, the Asian elephant is now extinct in West Asia, Java, and most of China (1). Remaining populations are highly fragmented with ongoing declines from habitat loss and poaching (2).

The only surviving members of the Proboscidea order, the elephantids first appeared in Africa 5-10 million years ago (3, 4). Asian elephants are most closely related to the extinct mammoths and are one of three remaining extant elephant species, along with the two species of African elephants (Loxodonta africana and Loxodonta cyclotis) (5).

Asian elephants have complex social interactions and live in small herds of related females. They communicate over long distances through low-pitched sound and olfactory cues, and use their trunks for tactile communication. As megaherbivores, Asian elephants range over large areas to graze on grass and browse, which can bring them into conflict with humans.

EEHV

Further hampering global elephant conservation efforts are infections from elephant endotheliotropic herpesviruses (EEHV). This widespread and highly fatal hemorrhagic disease is responsible for 80% of all Asian elephant calf fatalities, and results in the deaths of 1 in 5 elephants born in captivity (6, 7). Improved genomic resources for the Asian elephant may improve our understanding of the genetic factors that contribute to decreased susceptibility to EEHV infections, and may ultimately result in improved treatments.

Reviving the Woolly Mammoth

Woolly mammoths (Mammuthus primigenius) were cold-tolerant members of the elephant family that ranged across the Northern Hemisphere during the last ice age and went extinct between 4,000-10,000 years ago. Woolly mammoths had a number of adaptations to cold including dense, long hair, increased adipose tissue, shortened ears and tails, and hemoglobin polymorphisms that allowed them to thrive in the frigid mammoth steppe ecosystem (8, 9). Well preserved frozen remains found in the permafrost of Siberia and Alaska provide the rare opportunity to apply functional genomics to examine adaptive evolution in this extinct species. Since woolly mammoths were most closely related to the Asian elephant, this genome will allow us to better characterize the genetic changes that allowed this iconic species to thrive in the cold, and may one day allow us to de-extinct the species (10).

Assembly

Today, we share the chromosome-length assembly for the Asian elephant generated using samples donated by the Houston Zoo Asian elephant herd: Methai, Tupelo, Shanti, Tess, Thai, Tucker and Duncan. Check this live camera feed at the Zoo to meet the elephants! The assembly was generated using the $1K workflow, see (Dudchenko et al., 2018) for details.

One of the elephant's closest living relative is the rock hyrax, a small, furry herbivore native to Africa and the Middle East. Manatees and dugongs are also closely related to the elephant. The manatee, the rock hyrax and the elephant share a common ancestor, Tethytheria, which died out more than 50 million years ago. Despite initial appearances, hyraxes still have a few physical traits in common with elephants. These include tusks that grow from their incisor teeth (versus most mammals, which develop tusks from their canine teeth), flattened nails on the tips of their digits, and several similarities among their reproductive organs. See below how the new assembly relates to the chromosome-length rock hyrax genome assembly in the DNA Zoo collection (an upgrade from the draft assembly from Lindblad-Toh et al., 2011)!

Whole-genome alignment plot beetween the new Asian elephant genome assembly (Elephas_maximus_HiC) and the chromosome-length upgrade for the rock hyrax genome assembly (Pcap_2.0_HiC).

REFERENCES

1. A. Choudhury, Lahiri Choudhury, D.K., Desai, A., Duckworth, J.W., Easa, P.S., Johnsingh, A.J.T., Fernando, P., Hedges, S., Gunawardena, M., Kurt, F., Karanth, U., Lister, A., Menon, V., Riddle, H., Rübel, A. & Wikramanayake, E., Elephas maximus . The IUCN Red List of Threatened Species 2008: e.T7140A12828813. http://dx.doi.org/10.2305/IUCN.UK.2008.RLTS.T7140A12828813.en (2008).

2. S. H. Blake, S., Sinking the Flagship: the Case of Forest Elephants in Asia and Africa. Conservation Biology 18, 1191-1202 (2004).

3. J. Shoshani, Understanding proboscidean evolution: a formidable task. Trends Ecol Evol 13, 480-487 (1998).

4. V. J. Maglio, Origin and evolution of the Elephantidae, Transactions of the American Philosophical Society, (American Philosophical Society, Philadelphia,, 1973), pp. 149 p.

5. E. Palkopoulou et al., A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci U S A 115, E2566-E2574 (2018).

6. L. K. Richman et al., Elephant endotheliotropic herpesviruses EEHV1A, EEHV1B, and EEHV2 from cases of hemorrhagic disease are highly diverged from other mammalian herpesviruses and may form a new subfamily. J Virol 88, 13523-13546 (2014).

7. S. Srivorakul et al., Possible roles of monocytes/macrophages in response to elephant endotheliotropic herpesvirus (EEHV) infections in Asian elephants (Elephas maximus). PLoS One 14, e0222158 (2019).

8. K. L. Campbell et al., Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nat Genet 42, 536-540 (2010).

9. V. J. Lynch et al., Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Rep 12, 217-228 (2015).

10. G. M. Church, E. Regis, Regenesis : how synthetic biology will reinvent nature and ourselves (Basic Books, New York, 2012), pp. ix, 284 p.

Image: https://www.britannica.com/animal/elephant-mammal#/media/1/184366/53263

A nosey mouse

Welcome to the Year of the Rat! In Chinese culture, rats are a sign of wealth and abundance and similarly, rodents are the most abundant and species rich order of mammals, representing 40% of all extant mammals. Shockingly, there are comparatively few rodent genomes available relative to larger, more charismatic mega-fauna like cats and dogs.

We are excited to launch 2020 and the Year of the Rat with the release of the Northern rock mouse Peromyscus nasutus (Allen 1981) genome assembly, adding to a much-needed repertoire of rodent genomes that can now be used in human biomedical research and comparative genomics. The Criceidae family of rodents, to which P. nasutus belongs, includes almost 600 species of true hamsters, voles, lemmings, and New World rats and mice – the second-largest family of mammals.

Peromyscus nasutus has a long and slender nose relative to other Peromyscus species, but it would be otherwise hard to distinguish if not for its 'nosey' appearance (nasus means 'nose' in Latin). As the common name suggests, the northern rock mouse loves rocks and doesn't live too far from rocky areas in the Southern United States (mostly Colorado and New Mexico) and Mexico. The information contained in its scientific and common names, pointing to a long-nosed rock-loving mouse, is pretty much all we know about this species, starting from 'is this a species'?

In fact, the taxonomy of the Northern rock mouse has been subject of debate for decades. Previously recognized as a subspecies of Peromyscus difficilis, genetic inquiry has recently elevated it to the full-species level and this new assembly expands opportunities for further systematic inquiry. Will P. nasatus continue to be recognized as a species, or will it be demoted to just a population of Peromyscus difficilis, a closely related species?

The tissue sample was loaned to the MacManes lab by the Museum of Southwestern Biology, as part of a larger study on how desert mammals survive intense heat and drought. It was collected in 2017 in El Malpais National Conservation Area, Cibola County, New Mexico, USA by Kayce Bell and colleagues. The full collection record can be found at http://arctos.database.museum/guid/MSB:Mamm:299083.