1,666
Views
4
CrossRef citations to date
0
Altmetric
Mito Communication

Screening for the ancient polar bear mitochondrial genome reveals low integration of mitochondrial pseudogenes (numts) in bears

ORCID Icon, ORCID Icon, , & ORCID Icon
Pages 251-254 | Received 20 Dec 2016, Accepted 10 Apr 2017, Published online: 27 Apr 2017

References

  • Bensasson D, Zhang D-X, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol. 16:314–321.
  • Dayama G, Emery SB, Kidd JM, Mills RE. 2014. The genomic landscape of polymorphic human nuclear mitochondrial insertions. Nucleic Acids Res. 42:12640–12649.
  • Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O’Connell TC, Coxon P, Monaghan N, et al. 2011. Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol. 21:1251–1258.
  • Gordon D, Huddleston J, Chaisson MJP, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Dunn C, et al. 2016. Long-read sequence assembly of the gorilla genome. Science (NY). 352:aae0344.
  • Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – a baiting and iterative mapping approach. Nucleic Acids Res. 41:e129.
  • Hailer F, Kutschera VE, Hallström BM, Klassert D, Fain SR, Leonard JA, Arnason U, Janke A. 2012. Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science. 336:344–347.
  • Hazkani-Covo E, Zeller RM, Martin W. 2010. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genetics. 6:e1000834.
  • Kolokotronis S-O, Macphee RDE, Greenwood AD. 2007. Detection of mitochondrial insertions in the nucleus (numts) of pleistocene and modern muskoxen. BMC Evol Biol. 7:67.
  • Kumar V, Lammers F, Bidon T, Pfenniger M, Kolter L, Nilsson MA, Janke A. 2017. The evolutionary history of bears is characterized by gene flow across species. Scientific Reports. 7:46487.
  • Kurtén B, Anderson A. 1980. Pleistocene mammals of North America. J Mammal. 62:653–654.
  • Layer RM, Chiang C, Quinlan AR, Hall IM. 2014. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15:R84.
  • Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, et al. 2010a. The sequence and de novo assembly of the giant panda genome. Nature. 463:311–317.
  • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, et al. 2010b. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272.
  • Lindqvist C, Schuster SC, Sun Y, Talbot SL, Qi J, Ratan A, Tomsho LP, Kasson L, Zeyl E, Aars J, et al. 2010. Complete mitochondrial genome of a pleistocene jawbone unveils the origin of polar bear. Proc Nat Acad Sci USA. 107:5053–5057.
  • Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, et al. 2014. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell. 157:785–794.
  • Lopez JV, Yuhki N, Masuda R, Modi W, Brien SJO. 1994. Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol. 39:174–190.
  • Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, et al. 2012. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc Natl Acad Sci. 109:E2382–E2390.
  • Nowak RM. 1999. Walker’s mammals of the world. 6th ed. Baltimore: Johns Hopkins University Press.
  • Rogers HH, Griffith-Jones S. 2012. Mitochondrial pseudogenes in the nuclear genomes of drosophila. PLoS One. 7:e32593.
  • Sohn J-i, Nam J-W. 2016. The present and future of de novo whole-genome assembly. Brief Bioinformatics. October, bbw096.