The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis

Taylor, Gregory A.; Kirk, Heather; Coombe, Lauren; Jackman, Shaun D.; Chu, Justin; Tse, Kane; Cheng, Dean; Chuah, Eric; Pandoh, Pawan; Carlsen, Rebecca; Zhao, Yongjun; Mungall, Andrew J.; Moore, Richard A.; Birol, İnanç; Franke, Maria; Marra, Marco A.; Dutton, Christopher J.; Jones, Steven J.M.

doi:10.3390/genes9120598

Cited by 34 publications

(34 citation statements)

References 16 publications

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“…Since human mass production of antibiotics started in the 1940s, AMR has been increasing and now poses a serious global public health threat ( Crofts et al. 2017 ; Thorpe et al. 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

Brealey

Leitão

Valk

et al. 2020

Molecular Biology and Evolution

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Abstract Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

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“…Since human mass production of antibiotics started in the 1940s, AMR has been increasing and now poses a serious global public health threat ( Crofts et al. 2017 ; Thorpe et al. 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

Brealey

Leitão

Valk

et al. 2020

Molecular Biology and Evolution

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“…Brown bear individuals originated from the USA (Montana, Alaska), Sweden, Finland, Italy, Greece, Slovakia, Spain, Slovenia, Georgia, and Russia (genomewide coverage of 2.7x -58.2x). The recently published brown bear reference genome individual was excluded from the analysis due to unknown provenance [22].…”

Section: Methodsmentioning

confidence: 99%

Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role

2020

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Background: Polar bears are uniquely adapted to an Arctic existence. Since their relatively recent divergence from their closest living relative, brown bears, less than 500,000 years ago, the species has evolved an array of novel traits suited to its Arctic lifestyle. Previous studies sought to uncover the genomic underpinnings of these unique characteristics, and disclosed the genes showing the strongest signal of positive selection in the polar bear lineage. Here, we survey a comprehensive dataset of 109 polar bear and 33 brown bear genomes to investigate the genomic variants within these top genes present in each species. Specifically, we investigate whether fixed homozygous variants in polar bears derived from selection on standing variation in the ancestral gene pool or on de novo mutation in the polar bear lineage. Results: We find that a large number of sites fixed in polar bears are biallelic in brown bears, suggesting selection on standing variation. Moreover, we uncover sites in which polar bears are fixed for a derived allele while brown bears are fixed for the ancestral allele, which we suggest may be a signal of de novo mutation in the polar bear lineage. Conclusions: Our findings suggest that, among other mechanisms, natural selection acting on changes in genes derived from a combination of variation already in the ancestral gene pool, and from de novo missense mutations in the polar bear lineage, may have enabled the rapid adaptation of polar bears to their new Arctic environment.

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“…A black spruce needle tissue sample (genotype 40-10-1) was collected in Thunder Bay, Ontario (50°57′39.96″N, 90°27′20.16″E; elevation 741 m). Following nucleus purification, genomic DNA was extracted by Bio S&T using a cetyltrimethylammonium bromide (CTAB)/chloroform method, yielding 60 μg of high-quality purified DNA ( 4 , 5 ). A sequencing library was prepared using the Chromium linked-read platform from 10X Genomics ( 5 ) and sequenced with paired-end 150-base pair reads on an Illumina HiSeq X instrument at Canada’s Michael Smith Genome Sciences Centre.…”

Section: Announcementmentioning

confidence: 99%

Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada

Coombe

Lin

et al. 2020

Microbiol Resour Announc

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The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis

Cited by 34 publications

References 16 publications

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role

Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada

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