Chewsing a better assembly for COVID-19 research
Updated: Jul 7, 2021
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.
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
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