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  • 1. Faurby, Søren
    et al.
    Werdelin, Lars
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Svenning, Jens-Christian
    The difference between trivial and scientific names: There were never any true cheetahs in North America2016Inngår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760XArtikkel i tidsskrift (Annet vitenskapelig)
    Fulltekst (pdf)
    fulltext
  • 2. Meadows, Jennifer R. S.
    et al.
    Kidd, Jeffrey M.
    Wang, Guo-Dong
    Parker, Heidi G.
    Schall, Peter Z.
    Bianchi, Matteo
    Christmas, Matthew J.
    Bougiouri, Katia
    Buckley, Reuben M.
    Hitte, Christophe
    Nguyen, Anthony K.
    Wang, Chao
    Jagannathan, Vidhya
    Niskanen, Julia E.
    Frantz, Laurent A. F.
    Arumilli, Meharji
    Hundi, Sruthi
    Lindblad-Toh, Kerstin
    Ginja, Catarina
    Agustina, Kadek Karang
    André, Catherine
    Boyko, Adam R.
    Davis, Brian W.
    Drögemüller, Michaela
    Feng, Xin-Yao
    Gkagkavouzis, Konstantinos
    Iliopoulos, Giorgos
    Harris, Alexander C.
    Hytönen, Marjo K.
    Kalthoff, Daniela C.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Liu, Yan-Hu
    Lymberakis, Petros
    Poulakakis, Nikolaos
    Pires, Ana Elisabete
    Racimo, Fernando
    Ramos-Almodovar, Fabian
    Savolainen, Peter
    Venetsani, Semina
    Tammen, Imke
    Triantafyllidis, Alexandros
    vonHoldt, Bridgett
    Wayne, Robert K.
    Larson, Greger
    Nicholas, Frank W.
    Lohi, Hannes
    Leeb, Tosso
    Zhang, Ya-Ping
    Ostrander, Elaine A.
    Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture2023Inngår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 24, nr 1, artikkel-id 187Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background

    The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.

    Results

    We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.

    Conclusions

    We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

    Fulltekst (pdf)
    fulltext
  • 3. Pochon, Zoé
    et al.
    Bergfeldt, Nora
    Kırdök, Emrah
    Vicente, Mário
    Naidoo, Thijessen
    van der Valk, Tom
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Altınışık, N. Ezgi
    Krzewińska, Maja
    Dalén, Love
    Götherström, Anders
    Mirabello, Claudio
    Unneberg, Per
    Oskolkov, Nikolay
    aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow2023Inngår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 24, nr 1, artikkel-id 242Artikkel i tidsskrift (Fagfellevurdert)
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