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Complete mitogenome of Ganges river dolphin, Platanista gangetica gangetica and its phylogenetic relationship with other cetaceans

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Abstract

The Ganges river dolphin, Platanista gangetica gangetica is one of the endangered cetaceans. Due to increasing anthropogenic activities, it has faced a significant reduction in distribution range since the late 1800s and has even gone extinct from most of the early localities. The investigation of complete mitogenome holds significant relevance for identifying evolutionary relationships and monitoring the endangered species. Herein, we report and characterize for the first time the 16,319 bp complete mitochondrial genome of P. g. gangetica. It comprises 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region (CR). The genome composition was A + T biased (59.6%) and exhibited a positive AT-skew (0.104) and negative GC-skew (− 0.384). All the genes were encoded on the heavy strand, except eight tRNAs and the ND6 gene. In the CR, an 18 bp tandem repeat sequence was observed. Our Bayesian Inference (BI) and Maximum Likelihood (ML) based phylogenetic analysis indicated that studied river dolphins were polyphyletic and the placement of Platanista was to be more basal than other river dolphins (Lipotes, Inia and Pontoporia). The pairwise genetic distance of Platanista with other cetaceans was varied, with an overall close affinity with whales. The model-based BI and ML phylogenetic analysis indicated that Platanista clustering with Ziphiidae with high to moderate supportive values (PP/BP = 98/68). The results of this study provide insights important for the conservation genetics and further evolutionary studies of the freshwater river dolphins.

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References

  1. Sinha RK, Smith BD, Sharma G, Prasad G, Choudhury BC, Sapkota K, Sharma RK, Behera SK (2000) Status and distribution of the Ganges susu (Platanista gangetica) in the Ganges River system of India and Nepal. Occas Pap IUCN Species Surviv Comm 23:54–61

    Google Scholar 

  2. Smith BD, Ahmed B, Ali ME, Braulik G (2001) Status of the Ganga river dolphin or shushuk Platanista gangetica in Kaptai Lake and the southern rivers of Bangladesh. Oryx 35:61–72

    Article  Google Scholar 

  3. Sinha RK, Kannan K (2014) Ganga River dolphin: an overview of biology, ecology, and conservation status in India. Ambio 43:1029–1046

    Article  Google Scholar 

  4. The World Bank Report No. STEP705. The National Ganga River Basin Project 2011.

  5. Jones S (1982) The present status of the Gangetic susu, Platanista gangetica (Roxburgh), with comments on the Indus susu, P. minor Owen. FAO Fish Ser 5:97–115

    Google Scholar 

  6. Sinha RK, Sharma G (2003) Current status of the Ganga river dolphin, Platanista gangetica in the rivers Kosi and Son, Bihar, India. J Bombay Natl Hist Soc 100:27–37

    Google Scholar 

  7. Braulik GT, Smith BD (2019) Platanista gangetica (amended version of 2017 assessment). The IUCN Red List of Threatened Species. e.T41758A151913336.

  8. Cassens I, Vicario S, Waddell VG, Balchowsky H, Van Belle D, Ding W, Fan C, Mohan RL, Simões-Lopes PC, Bastida R, Meyer A (2000) Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proc Natl Acad Sci 97:11343–11347

    Article  CAS  Google Scholar 

  9. Messenger SL (1994) Phylogenetic relationships of platanistoid river dolphins (Odontoceti, Cetacea): assessing the significance of fossil taxa. Proc San Diego Soc Natl Hist 29:125–133

    Google Scholar 

  10. Árnason Ú, Gullberg A (1996) Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans. Mol Biol Evol 13:407–417

    Article  Google Scholar 

  11. Hamilton H, Caballero S, Collins AG, Brownell RL Jr (2001) Evolution of river dolphins. Proc R Soc Lond B 268:549–556

    Article  CAS  Google Scholar 

  12. Yan J, Zhou K, Yang G (2005) Molecular phylogenetics of ‘river dolphins’ and the baiji mitochondrial genome. Mol Phylogenet Evol 37:743–750

    Article  CAS  Google Scholar 

  13. Avise JC (1989) A role for molecular genetics in the recognition and conservation of endangered species. Trends Ecol Evol 4:279–281

    Article  CAS  Google Scholar 

  14. Hoelzel AR, Natoli A, Dahlheim ME, Olavarria C, Baird RW, Black NA (2002) Low worldwide genetic diversity in the killer whale (Orcinus orca): implications for demographic history. Proc R Soc 269:1467–1473

    Article  Google Scholar 

  15. Morin PA, Archer FI, Foote AD, Vilstrup J, Allen EE, Wade P, Durban J, Parsons K, Pitman R, Li L, Bouffard P (2010) Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Res 20(7):908–916

    Article  CAS  Google Scholar 

  16. DeFilippis VR, Moore WS (2000) Resolution of phylogenetic relationships among recently evolved species as a function of amount of DNA sequence: an empirical study based on woodpeckers (Aves: Picidae). Mol Phylogenet Evol 16:143–160

    Article  CAS  Google Scholar 

  17. Rokas A, Carroll SB (2005) More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 22:1337–1344

    Article  CAS  Google Scholar 

  18. Hassanin A, Ropiquet A, Couloux A, Cruaud C (2009) Evolution of the mitochondrial genome in mammals living at high altitude: new insights from a study of the tribe Caprini (Bovidae, Antilopinae). J Mol Evol 68:293–310

    Article  CAS  Google Scholar 

  19. 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 69:313–319

    Article  Google Scholar 

  20. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, Nishida M (2013) MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–2540

    Article  CAS  Google Scholar 

  21. Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181–W184

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  23. Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol 41:353–358

    Article  CAS  Google Scholar 

  24. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res 31(1):28–33

    Article  CAS  Google Scholar 

  25. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580

    Article  CAS  Google Scholar 

  26. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973

    Article  CAS  Google Scholar 

  27. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772

    Article  CAS  Google Scholar 

  28. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol 67(5):901

    Article  CAS  Google Scholar 

  29. Edler D, Klein J, Antonelli A, Silvestro D (2019) raxmlGUI 2.0 beta: a graphical interface and toolkit for phylogenetic analyses using RAxML. BioRxiv. https://doi.org/10.1101/800912

    Article  Google Scholar 

  30. Campanella JJ, Bitincka L, Smalley J (2003) MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinform 4:1–4

    Article  Google Scholar 

  31. Arnason U, Gullberg A, Janke A (2004) Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene 333:27–34

    Article  CAS  Google Scholar 

  32. Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780

    Article  CAS  Google Scholar 

  33. Kumar A, Gautam KB, Singh B, Yadav P, Gopi GV, Gupta SK (2019) Sequencing and characterization of the complete mitochondrial genome of Mishmi takin (Budorcas taxicolor taxicolor) and comparison with the other Caprinae species. Int J Biol Macromol 137:87–94

    Article  CAS  Google Scholar 

  34. Arif IA, Khan HA (2009) Molecular markers for biodiversity analysis of wildlife animals: a brief review. Anim Biodivers Conserv 32(1):9–17

    Google Scholar 

  35. Stoneking M, Hedgecock D, Higuchi RG, Vigilant L, Erlich HA (1991) Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 48:370

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Gupta SK, Kumar A, Angom A, Singh B, Ghazi MG, Tuboi C, Hussain SA (2018) Genetic analysis of endangered hog deer (Axis porcinus) reveals two distinct lineages from the Indian subcontinent. Sci Rep 8:16308

    Article  Google Scholar 

  37. Gupta SK, Kumar A, Gaur A, Hussain SA (2015) Detection of 40 bp insertion-deletion (INDEL) in mitochondrial control region among sambar (Rusa unicolor) populations in India. BMC Res Notes 8:1–7

    Article  Google Scholar 

  38. Yang XG (2009) Bayesian inference of cetacean phylogeny based on mitochondrial genomes. Biologia 64:811–818

    CAS  Google Scholar 

  39. Verma SK, Sinha RK, Singh L (2004) Phylogenetic position of Platanista gangetica: insights from the mitochondrial cytochrome b and nuclear interphotoreceptor retinoid-binding protein gene sequences. Mol Phylogenet Evol 33:280–288

    Article  CAS  Google Scholar 

  40. Nikaido M, Matsuno F, Hamilton H, Brownell RL, Cao Y, Ding W, Zuoyan Z, Shedlock AM, Fordyce RE, Hasegawa M, Okada N (2001) Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc Natl Acad Sci 98:7384–7389

    Article  CAS  Google Scholar 

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Acknowledgement

We acknowledge the support provided by Dr. Dhananjai Mohan, Director and Dr. Y.V. Jhala, Dean, WII and the entire project team of NMCG. We thank the state forest departments of Uttar Pradesh and Bihar Pradesh for their support.

Funding

This study was funded by the National Mission for Clean Ganga (NMCG) project of the Ministry of Jal Shakti through Grant Number B/02/2015-16/1259/NMCG.

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  1. Ajit Kumar and Prabhaker Yadav have been equally contributed to this article.

Authors and Affiliations

  1. Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, 248 001, India

    Ajit Kumar, Prabhaker Yadav, Aftab Usmani, Syed Ainul Hussian & Sandeep Kumar Gupta

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  1. Ajit Kumar
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  2. Prabhaker Yadav
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  3. Aftab Usmani
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Correspondence to Sandeep Kumar Gupta.

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Kumar, A., Yadav, P., Usmani, A. et al. Complete mitogenome of Ganges river dolphin, Platanista gangetica gangetica and its phylogenetic relationship with other cetaceans. Mol Biol Rep 48, 315–322 (2021). https://doi.org/10.1007/s11033-020-06048-4

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