A spectacular bear assembly

The spectacled bear (Tremarctos ornatus) is the only bear native to South America. It is the last remaining short-faced bear (subfamily Tremarctinae). The species is classified as Vulnerable by the IUCN because of habitat loss.

Handsome Chester, photo by Valerie [CC BY-NC-ND 2.0], via flickr.com

The species is of course famous in literary circles as much as in conservation ones thanks to Michael Bond's much-loved Paddington, whose adventures have featured in twenty books, three TV series and two feature films to date. (Interestingly, Bond originally imagined Paddington to have 'travelled all the way from darkest Africa', before being advised that there were no bear species in Africa! So the bear became one from 'darkest Peru').

Today, we share the chromosome-length genome assembly for the spectacled bear, based on a sample provided to us by the San Antonio Zoo. This is a $1K-model genome assembly, with contig N50=117kb and scaffold N50=105Mb. Read more about the $1K genomes on our Methods page.

This is our 5th genome in the Ursidae family (bears), after the Malayan sun bear, the American black bear, grizzly and polar bear. Unlike all the other bears who all have a karyotype of 2n=74, the spectacled bear is 2n=52. See below how the chromosomes of the spectacled bear relate to the very conservative karyotype of all other bears, suggesting multiple fusion events associated with the spectacled bear chromosomes as compared to the 'main' Ursidae karyotype!

Whole-genome alignment plots between the chromosome-length spectacled bear assembly and those of other bears in the DNA Zoo collection: left to right, Ursus americanus, Ursus arctos, Helarctos malayanus and Ursus maritimus. The Helarctos malayanus alignments are filtered at a higher threshold to account for shorter phylogenetic distance between the species.

Don't forget to check out the interactive map for the 2n=52 chromosomes below and on the corresponding assembly page!

Clever clovers

Sustainable agricultural production entails growing food without damaging the underlying soil. Legumes are of great interest for such efforts: because they produce their own nitrogen via symbiotic nitrogen fixation, legumes can actually improve the soil.

Among legumes, pasture or forage legumes tend to be more resilient to stress and more capable of thriving in marginal land. These forage legumes are highly valued feed for extensive livestock production. There is an increasing interest worldwide in using annual forage legumes as cover crops to supply soil nitrogen. Symbiotic nitrogen fixation in legumes leads to high protein fodder content and rejuvenated soils for a sustainable feed system.

Photo Description – The subterranean clover (Trifolium subterraneum) cv Daliak. Photo Credits and acknowledgements – Dr Parwinder Kaur [CC]

Clovers are among the most effective to break the ‘infernal circle of the fallow’ a technique known to the Germans as ‘Besömmerung’. Subterranean clover (Trifolium subterraneum L.) makes the greatest contribution to livestock feed production and soil improvement in terms of total worldwide usage among annual clovers, particularly in Australia, where it is sown over 29 million hectares. The self-reseeding ability and grazing tolerance of subterranean clover, even under suboptimal and variable environmental conditions, contribute to its widespread distribution.

Subterranean clover is a diploid (2n = 2x = 16), predominantly inbreeding, annual species with a relatively small genome size of 540 Mbp (1C = 0.55 pg DNA) that can be readily hybridized, and exhibits wide diversity for both qualitative and quantitative agronomic and morphological characters. Within the genus Trifolium, it is established as a reference species for genetic and genomic studies.

Today, we add the subterranean clover chromosome-length resource to the DNA Zoo website. The assembly is described in more detail in our 2018 preprint on the subject.

The Hi-C work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. The following people contributed to the Hi-C chromosome-length upgrade of the project: Christopher Lui, Melanie Pham, Olga Dudchenko, Erez Aiden & Parwinder Kaur.

Chewsing a better assembly for COVID-19 research

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.