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Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences

  • 1.

    Garshelis, D. & Steinmetz, R. Ursus thibetanus. The IUCN Red List of Threatened Species 2016. https://dx.doi.org/Downloaded on 17 January 2020 (2016).

  • 2.

    Parter, S. H. The Book of Indian Animal (Bombay Natural History Society and Oxford University Press, India, 1980).

    Google Scholar 

  • 3.

    Sathyakumar, S. & Choudhury, A. Distribution and status of asiatic black bear in India. J. Bomb. Nat. Hist. Soci. 104, 316–323 (2007).

    Google Scholar 

  • 4.

    Pocock, R. I. The Fauna of British India, Including Ceylon and Burma, Mammalia Vol. 2 (Taylor and Francis, London, 1941).

    Google Scholar 

  • 5.

    Sathyakumar, S., Kaul, R., Ashraf, N. V. K., Mookerjee, A. & Menon, V. National Bear Conservation and Welfare Action Plan (Ministry of Environment and Forest, Wildlife Institute of India and Wildlife Trust of India, 2012).

    Google Scholar 

  • 6.

    Charoo, S.A., Sharma, L.K. & Sathyakumar, S. Asiatic Black Bear—Human Conflicts around Dachigam National Park, Kashmir. Technical Report. Wildlife Institute of India, Dehradun. 29 (2009).

  • 7.

    Hou, W. R. et al. A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis). Int. J. Biol. Sci. 3, 85–90 (2007).

    CAS  Article  Google Scholar 

  • 8.

    Yu, L. et al. Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evol. Biol. 7, 198 (2007).

    Article  Google Scholar 

  • 9.

    Hwang, D. S. et al. A comprehensive analysis of three Asiatic black bear mitochondrial genomes (subspecies ussuricus, formosanus and mupinensis), with emphasis on the complete mtDNA sequence of Ursus thibetanus ussuricus (Ursidae). Mitochondrial. DNA 19, 418–429 (2008).

    CAS  PubMed  Google Scholar 

  • 10.

    Kadariya, R. et al. High genetic diversity and distinct ancient lineage of Asiatic black bears revealed by non-invasive surveys in the Annapurna Conservation Area Nepal. PLoS ONE 13, 0207622 (2018).

    Google Scholar 

  • 11.

    Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135–1145 (2008).

    CAS  Article  Google Scholar 

  • 12.

    Ekblom, R. & Galindo, J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) 107, 1–15 (2011).

    CAS  Article  Google Scholar 

  • 13.

    Edwards, S. V., Shultz, A. J. & Campbell-Staton, S. C. Next-generation sequencing and the expanding domain of phylogeography. Folia Zool. 64, 187–206 (2015).

    Article  Google Scholar 

  • 14.

    Natesh, M. et al. Conservation priorities for endangered Indian tigers through a genomic lens. Sci. Rep. 7, 9614 (2017).

    ADS  Article  Google Scholar 

  • 15.

    Song, N., Cai, W. & Li, H. Deep-level phylogeny of Cicadomorpha inferred from mitochondrial genomes sequenced by NGS. Sci. Rep. 7, 10429 (2017).

    ADS  Article  Google Scholar 

  • 16.

    Delisle, I. & Strobeck, C. Conserved primers for rapid sequencing of the complete mitochondrial genome from carnivores, applied to three species of bears. Mol. Biol. Evol. 19, 357–361 (2002).

    CAS  Article  Google Scholar 

  • 17.

    Van Dijk, E., Auger, H., Jaszczyszyn, Y. & Thermes, C. T. years of next-generation sequencing technology. Trends Genet. 30(9), 418–426 (2014).

    Article  Google Scholar 

  • 18.

    Heather, J. & Chain, B. The sequence of sequencers: the history of sequencing DNA. Genomics 107(1), 1–8 (2016).

    CAS  Article  Google Scholar 

  • 19.

    Wang, S., Wang, B., Wang, F. & Wu, Z. Complete mitochondrial genome of Gallus domesticus (Galliformes: Phasianidae). Mitochondrial. DNA A DNA Mapp. Seq. Anal. 27(2), 978–979 (2016).

    Article  Google Scholar 

  • 20.

    Zhou, M., Yu, J., Li, J., Ouyang, B. & Yang, J. The complete mitochondrial genome of Budorcas taxicolor tibetana (Artiodactyla: Bovidae) and comparison with other Caprinae species: Insight into the phylogeny of the genus Budorcas Int. J. Biol. Macromol. 121, 223–232 (2019).

    CAS  Article  Google Scholar 

  • 21.

    Kamalakkannan, R. et al. The complete mitochondrial genome of Indian gaur, Bos gaurus and its phylogenetic implications. Sci. Rep. 10, 11936. https://doi.org/10.1038/s41598-020-68724-6 (2020).

    ADS  CAS  Article  PubMed  PubMed Central  Google Scholar 

  • 22.

    Hahn, C., Bachmann, L. & Chevreux, B. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – a baiting and iterative mapping approach. Nucleic Acids Res. 41, 129 (2013).

    Article  Google Scholar 

  • 23.

    Boore, J. L. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767–1780 (1999).

    CAS  Article  Google Scholar 

  • 24.

    Feng, H., Feng, C., Wang, L. & Huang, Y. Complete mitochondrial genome of the golden takin (Budorcas taxicolor bedfordi). Mitochondrial. DNA 1, 186–188 (2016).

    Article  Google Scholar 

  • 25.

    Kumar, A. et al. Sequencing and characterization of the complete mitochondrial genome of Mishmi takin (Budorcas taxi color taxicolor) and comparison with the other Caprinae species. Int. J. Biol. Macromol. 137, 87–94 (2019).

    CAS  Article  Google Scholar 

  • 26.

    Sarvani, R. K. et al. Characterization of the complete mitogenome of Indian Mouse Deer, Moschiola indica (Artiodactyla: Tragulidae) and its evolutionary significance. Sci. Rep. 8, 2697 (2018).

    ADS  Article  Google Scholar 

  • 27.

    Lan, T. et al. Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya region and the identity of the yeti. Proc. R. Soc. B 284, 20171804 (2017).

    Article  Google Scholar 

  • 28.

    Jiagi, W. et al. Phylogeographic and demographic analysis of the Asian Black Bear (Ursus thibetanus) based on Mitochondrial DNA. PLoS ONE 10, e0136398 (2015).

    Article  Google Scholar 

  • 29.

    Timmermans, M. J. et al. Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res. 38, e197 (2010).

    CAS  Article  Google Scholar 

  • 30.

    Cabrera-Brandt, M. A. & Gaitan-Espitia, J. D. Phylogenetic analysis of the complete mitogenome sequence of the raspberry weevil Aegorhinus superciliosus (Coleoptera: Curculionidae), supports monophyly of the tribe Aterpini. Gene 571, 205–211 (2015).

    CAS  Article  Google Scholar 

  • 31.

    Grant, J. R. & Stothard, P. The CGView Server: a comparative genomics tool for circular 423 genomes. Nucleic Acids Res. 36, 181–184 (2008).

    Article  Google Scholar 

  • 32.

    Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).

    CAS  Article  Google Scholar 

  • 33.

    Perna, N. T. & Kocher, T. D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41, 353–358 (1995).

    ADS  CAS  Article  Google Scholar 

  • 34.

    Beier, S., Thiel, T., Munch, T., Scholz, U. & Mascher, M. MISA-web: a web server for microsatellite prediction. Bioinformatics 33, 2583–2585 (2017).

    CAS  Article  Google Scholar 

  • 35.

    Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 36, 573–580 (1999).

    Article  Google Scholar 

  • 36.

    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. Mega X: molecular evolutionary genetics analysis across computing platform. Mol. Biol. Evol. 35, 1547–1549 (2018).

    CAS  Article  Google Scholar 

  • 37.

    Mattei, E., Pietrosanto, M., Ferree, F. & Citterich, M. H. Web-Beagle: a web server for the alignment of RNA secondary structures. Nuc Acids Res. 43, 493–497 (2015).

    Article  Google Scholar 

  • 38.

    Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4, 1–5 (2018).

    Article  Google Scholar 

  • 39.

    Nylander, J.A.A. MrModelTest Version 2. Programme Distributed by the Author. Evolutionary Biology Centre, Uppsala University (2004).

  • 40.

    Wayne, R. K., Van, V. B. & O’Brien, S. J. Molecular distance and divergence time in carnivores and primates. Mol. Biol. Evol. 8, 297–319 (1991).

    CAS  PubMed  Google Scholar 

  • 41.

    Rambaut, A. FigTree, Version1.4.4. Available at: https://tree.bio.ed.ac.uk/software/figtree/. (2018).


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