Chewsing a better assembly for COVID-19 research

Updated: Jul 7

The Cricetinae subfamily of hamsters, part of the large family of mouse-like rodents, contains about 20 species in several genera (Macdonald, 2010; Wilson and Mittermeier, 2017), with the exact numbers being under dispute. Hamsters live in arid or semiarid areas, encompassing parts of Europe, the Middle East, Russia, and China. Mostly herbivorous, they range in size from 5 to 28 centimeters. The golden hamster (Mesocricetus auratus), with up to 16 cm body length and 175 g in weight, is now widely used as pet and laboratory animal. Captive populations descended from a female collected in 1930 in Syria, hence it is also termed Syrian hamster, and from additional animals caught in 1971. Lifespan is up to 2 years in the wild and up to 5 in captivity.

Golden hamster, Photo by Nana-ne from Pixabay [Pixabay License]

Hamsters use their characteristic cheek pouches to collect food, which is stored in burrows, and consumed during occasionally wakings during the hibernation period. In the wild, golden hamsters, like most hamster species are solitary and aggressive toward members of their own species (an exemption may be one dwarf hamster species, Phodopus campbelli, where male animals participate in child birth and raising, which in other hamster species is done by females alone). Closest observed distances between occupied burrows was 118 meters. Hamsters feature a strong sense of smell and hearing, which are both also important for communication. Although fought in some areas since considered pests to agriculture, most hamster species are not endangered since they live in regions inhospitable to humans, and show high reproduction rates (Macdonald, 2010; Wilson and Mittermeier, 2017). Golden hamsters, and particularly male animals, were shown to have a strong preference towards and tolerance for alcohol (Lee et al., 2001).


In the laboratory, golden hamsters are an important animal model to study infectious diseases and have been used to study a plethora of virus infections including important human pathogens such as influenza A viruses (Miao et al., 2019). Upon emergence of the first severe acute respiratory distress coronavirus (SARS-CoV) in 2002/2003, Syrian hamsters were established as a disease model for coronavirus infection (Roberts et al., 2005). Based on this knowledge, this hamster species quickly became important within the research of coronavirus disease 2019 (COVID-19), caused by a related virus, called SARS-CoV-2 (Osterrieder et al., 2020; Rosa et al., 2021; Sia et al., 2020). Within COVID-19 related research, this species is widely used for studies on pathogenesis, drug development, and vaccines (Kreye et al., 2020; Lee and Lowen, 2021; Yahalom-Ronen et al., 2020).


Back in 2019, we have shared a chromosome-length upgrade to MesAur1.0, a short-read draft genome assembly generated by the Broad Institute. Today, in collaboration with a team at Max Delbruck Center for Molecular Medicine and Free University Berlin led by Emanuel Wyler and including Tatiana Borodina, Claudia Quedenau, Janine Altmüller, Markus Landthaler, Jakob Trimpert and Sandro Andreotti, we improve the genomic resources available for the species by sharing a long-read-based de novo chromosome-length genome assembly (cN50=2Mb; sN50=110Mb). The long-read sequencing was done by the MDC team with Oxford Nanopore (Promethion), with about 30x coverage and 50 kB median length of the sequences, polished with Illumina WGS data, also generated by MDC. The draft assembly was generated using wtdbg2. Hi-C data were mapped to the draft genome assembly and processed with Juicer, scaffolded with 3d-dna, followed by manually curation in JBAT. For more information see our Methods page!


Check out the new and improved chromosome-length contact map (2n=44) below. Stay tuned for new and improved annotations!

Blog post by: Emanuel Wyler, with contributions from Zhenzhen Yang


References:

Kreye, J., Reincke, S.M., Kornau, H.C., Sanchez-Sendin, E., Corman, V.M., Liu, H., Yuan, M., Wu, N.C., Zhu, X., Lee, C.D., et al. (2020). A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model. Cell 183, 1058-1069 e1019.

Lee, C.Y., and Lowen, A.C. (2021). Animal models for SARS-CoV-2. Curr Opin Virol 48, 73-81.

Lee, S.F., Chen, Z.Y., and Fong, W.P. (2001). Gender difference in enzymes related with alcohol consumption in hamster, an avid consumer of alcohol. Comp Biochem Physiol C Toxicol Pharmacol 129, 285-293.

Macdonald, D.W., ed. (2010). The encyclopedia of mammals (Oxford New York: Oxford New York : Oxford University Press).

Miao, J., Chard, L.S., Wang, Z., and Wang, Y. (2019). Syrian Hamster as an Animal Model for the Study on Infectious Diseases. Front Immunol 10, 2329.

Osterrieder, N., Bertzbach, L.D., Dietert, K., Abdelgawad, A., Vladimirova, D., Kunec, D., Hoffmann, D., Beer, M., Gruber, A.D., and Trimpert, J. (2020). Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters. Viruses 12.

Roberts, A., Vogel, L., Guarner, J., Hayes, N., Murphy, B., Zaki, S., and Subbarao, K. (2005). Severe acute respiratory syndrome coronavirus infection of golden Syrian hamsters. J Virol 79, 503-511.

Rosa, R.B., Dantas, W.M., do Nascimento, J.C.F., da Silva, M.V., de Oliveira, R.N., and Pena, L.J. (2021). In Vitro and In Vivo Models for Studying SARS-CoV-2, the Etiological Agent Responsible for COVID-19 Pandemic. Viruses 13.

Sia, S.F., Yan, L.M., Chin, A.W.H., Fung, K., Choy, K.T., Wong, A.Y.L., Kaewpreedee, P., Perera, R., Poon, L.L.M., Nicholls, J.M., et al. (2020). Pathogenesis and transmission of SARS-CoV-2 in golden hamsters. Nature 583, 834-838.

Wilson, D.E., and Mittermeier, R.A., eds. (2017). Handbook of the mammals of the world. Vol.7, Rodents II (Barcelona: Lynx Edicions : Conservation International : IUCN).

Yahalom-Ronen, Y., Tamir, H., Melamed, S., Politi, B., Shifman, O., Achdout, H., Vitner, E.B., Israeli, O., Milrot, E., Stein, D., et al. (2020). A single dose of recombinant VSV-G-spike vaccine provides protection against SARS-CoV-2 challenge. Nat Commun 11, 6402.

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