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Rapid Communication

The complete mitochondrial genome of an ancient cattle (Bos taurus) from Taosi site, China, and its phylogenetic assessment

ORCID Icon, , & ORCID Icon
Pages 804-806 | Received 08 Sep 2021, Accepted 30 Apr 2022, Published online: 10 May 2022

References

  • Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):804–319.
  • Brunson K, He N, Dai X. 2016. Sheep, cattle, and specialization: new zooarchaeological perspectives on the Taosi Longshan. Int J Osteoarchaeol. 26(3):460–475.
  • Cai D, Sun Y, Tang Z, Hu S, Li W, Zhao X, Xiang H, Zhou H. 2014. The origins of Chinese domestic cattle as revealed by ancient DNA analysis. J Archaeol Sci. 41:423–434.
  • Chen N, Cai Y, Chen Q, Li R, Wang K, Huang Y, Hu S, Huang S, Zhang H, Zheng Z, et al. 2018. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun. 9(1):2337.
  • Dabney J, Knapp M, Glocke I, Gansauge M-T, Weihmann A, Nickel B, Valdiosera C, García N, Pääbo S, Arsuaga J-L, et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A. 110(39):15758–15763.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9(8):772–772.
  • Felius M, Beerling M, Buchanan D, Theunissen B, Koolmees P, Lenstra J. 2014. On the history of cattle genetic resources. Diversity. 6(4):705–750.
  • Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. 2021. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ. 9(9):e10947.
  • Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 27(21):2987–2993.
  • Okonechnikov K, Conesa A, Garcia-Alcalde F. 2016. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 32(2):292–294.
  • Peltzer A, Jäger G, Herbig A, Seitz A, Kniep C, Krause J, Nieselt K.,. 2016. EAGER: efficient ancient genome reconstruction. Genome Biol. 17:60.
  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61(3):539–542.
  • Schubert M, Lindgreen S, Orlando L. 2016. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 9:88.
  • Srinivasan K, Bisson T, Goodson G, Voruganti K. 2012. iDedup: latency-aware, inline data deduplication for primary storage. Proceedings of the 2012 File and Storage Technologies Conference, p. 1–14.
  • Verdugo MP, Mullin VE, Scheu A, Mattiangeli V, Daly KG, Maisano Delser P, Hare AJ, Burger J, Collins MJ, Kehati R, et al. 2019. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science. 365(6449):173–176.