Best. Rupert. Ever.

The Indian rhino (Rhinoceros unicornis), also known as the greater one-horned rhino, is a rhinoceros native to the Indian subcontinent. Among terrestrial land mammals native to Asia, the Indian rhinoceros is second in size only to the Asian elephant and can weigh more than one ton! [1]

Indian rhinos are listed as a vulnerable species on the IUCN red list. This is actually good news: the greater one-horned rhino is one of Asia’s biggest success stories, with their status improving from endangered to vulnerable following significant population increases. However, the species still remains under threat from poaching for its horn and from habitat loss and degradation.

Today, we share the chromosome-length assembly for Rupert, an Indian rhino from the Oklahoma City Zoo. That’s him on the photo below and on the blog cover photo (with his mom). Isn’t he the cutie!

One could say Rupert was destined to be sequenced since his parents, Chandra and Niki, met because of their genetic compatibility! Today Rupert is part of the Greater One-Horned Rhinoceros Species Survival Plan (SSP) developed by the Association of Zoos and Aquariums. Today, Rupert lives at Mesker Park Zoo, Indiana. We thank Julia Jones, Liz McCrae, Jennifer D’Agostino and Candice Rennels at the Oklahoma City Zoo for their help with the sample. To learn more about the OKC Zoo visit www.okczoo.org.

This is a $1K genome assembly. For more details about the genome assembly procedure, see Dudchenko et al., 2018.

Rhino Rupert hopping, credit: Lena Kofoed, via Oklahoma City Zoo

Cover photo credits: Nicky and Rupert by Joel Sartore, via Oklahoma City Zoo

Rousette bats: a coronavirus reservoir

Today we release a chromosome-length genome assembly for the Madagascar rousette (Rousettus madagascariensis), a small Malagasy fruit bat, one of ten species in the genus. Rousettus is an old world fruit bat of the family Pteropodidae, like the Madagascar flying fox (Pteropus rufus), whose genome we released at the end of 2019.[i] Members of the family Pteropodidae have been known to be natural hosts for many different types of viruses.

We have worked to release this genome as soon as possible in light of the Wuhan coronavirus nCoV-2019 [ii], which, as of this writing, has infected over 17,000 people, with an early case fatality rate of approximately 2%.[iii] Two weeks ago, an analysis of Wuhan and SARS coronavirus genomes by Xu et al.[iv] came to the conclusion that the human viral sequence is most closely related to a nonhuman viral sequence known as HKU-9-1. HKU-9-1, also known as “Rousettus bat coronavirus”, was first isolated from a bat in genus Rousettus. As such we believe that the reference genome for a species in this genus – even one endemic to Madagascar rather than China – could be relevant to studies of the coronavirus and its reservoir.

Ekipa Fanihy (“Team Fruit Bat” in Malagasy, the native language of Madagascar), led by Dr. Cara Brook (https://carabrook.github.io/team.html) has been studying the dynamics of viral infection in Malagasy fruit bats since 2013. Old World Fruit Bats have been disproportionately linked to the emergence of human viruses in the past two decades, serving as reservoir hosts for rabies and related lyssaviruses, Hendra and Nipah henipaviruses, Ebola and Marburg filoviruses, and the SARS coronavirus[v] [vi]. Several genomic analyses have demonstrated unique adaptations related to the evolution of flight which appear to have elongated bat lifespans and also made them resilient to many of the pathogenic effects of viral hosting.[vii],[viii],[ix] It has also been demonstrated that several zoonotic virus families circulate specifically in the Malagasy bats.[x] DNA Zoo is assembling bat genomes, including all the Madagascar fruit bats, in order to learn more about the mechanisms which underlie these bats’ unique viral tolerance. If you have samples from potential bat vector species, we’d love to be in touch. (Aviva Presser Aiden - Aviva.Aiden@bcm.edu)

Assembly of this genome was financed by the DNA Zoo and NIH grant (R01-AI129822-01) administered by Dr. Jean-Michel Héraud of Institut Pasteur of Madagascar and Dr. Cara Brook of UC Berkeley (link: http://grantome.com/grant/NIH/R01-AI129822-01).

Ekipa Fanihy is affiliated with UC Berkeley (link: https://ib.berkeley.edu/), the University of Antananarivo (link: http://www.univ-antananarivo.mg/), and Institut Pasteur of Madagascar (link: http://www.pasteur.mg/).

Aviva Presser Aiden, Cara Brook, Olga Dudchenko

[i] E.C. Teeling, M.S. Springer, O. Madsen, P. Bates, S.J. O’brien, W.J. Murphy, A molecular phylogeny for bats illuminates biogeography and the fossil record., Science (80-. ). 307 (2005) 580–4. doi:10.1126/science.1105113.

[ii] Zhou, P. et al. “Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin” Biorxiv, doi: https://doi.org/10.1101/2020.01.22.914952

[iii] https://www.worldometers.info/coronavirus/ accessed 2/3/2020

[iv] Xu, X, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. SCIENCE CHINA Life Sciences; doi: 10.1007/s11427-020-1637-5

[v] C.H. Calisher, J.E. Childs, H.E. Field, K. V Holmes, T. Schountz, Bats: Important reservoir hosts of emerging viruses, Clin. Microbiol. Rev. 19 (2006) 531–45. doi:10.1128/CMR.00017-06.

[vi] C.E. Brook, A.P. Dobson, Bats as “special” reservoirs for emerging zoonotic pathogens, Trends Microbiol. 23 (2015) 172–180. doi:10.1016/j.tim.2014.12.004.

[vii] S.S. Pavlovich, S.P. Lovett, G. Koroleva, J.C. Guito, C.E. Arnold, E.R. Nagle, K. Kulcsar, A. Lee, F. Thibaud-Nissen, A.J. Hume, E. Mühlberger, L.S. Uebelhoer, J.S. Towner, R. Rabadan, M. Sanchez-Lockhart, T.B. Kepler, G. Palacios, The Egyptian Rousette genome reveals unexpected features of bat antiviral immunity, Cell. 173 (2018) 1–13. doi:10.1016/j.cell.2018.03.070

[viii] G. Zhang, C. Cowled, Z. Shi, Z. Huang, K. a Bishop-Lilly, X. Fang, J.W. Wynne, Z. Xiong, M.L. Baker, W. Zhao, M. Tachedjian, Y. Zhu, P. Zhou, X. Jiang, J. Ng, L. Yang, L. Wu, J. Xiao, Y. Feng, Y. Chen, X. Sun, Y. Zhang, G. a Marsh, G. Crameri, C.C. Broder, K.G. Frey, L.-F. Wang, J. Wang, Comparative analysis of bat genomes provides insight into the evolution of flight and immunity, Science. 339 (2013) 456–60. doi:10.1126/science.1230835.

[ix] I. Seim, X. Fang, Z. Xiong, A. V Lobanov, Z. Huang, S. Ma, Y. Feng, A. a Turanov, Y. Zhu, T.L. Lenz, M. V Gerashchenko, D. Fan, S. Hee Yim, X. Yao, D. Jordan, Y. Xiong, Y. Ma, A.N. Lyapunov, G. Chen, O.I. Kulakova, Y. Sun, S.-G. Lee, R.T. Bronson, A. a Moskalev, S.R. Sunyaev, G. Zhang, A. Krogh, J. Wang, V.N. Gladyshev, Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii., Nat. Commun. 4 (2013) 2212. doi:10.1038/ncomms3212.

[x] C.E. Brook, H.C. Ranaivoson, C.C. Broder, A.A. Cunningham, J.-M. Héraud, A.J. Peel, L. Gibson, J.L.N. Wood, C.J. Metcalf, A.P. Dobson, Disentangling serology to elucidate henipa- and filovirus transmission in Madagascar fruit bats, J. Anim. Ecol. 00 (2019) 1– 16. doi:10.1111/1365-2656.12985.

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)!