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Published March 30, 2023 | Version v1
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The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae

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Baeza, J. Antonio, Macdonald-Shedd, Austin, Latorre-Cárdenas, María Camila, Griffin, Erin, Gutiérrez-Rodríguez, Carla (2023): The first genomic resource for the 'near threatened' Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae. Journal of Natural History 57 (5-8): 408-425, DOI: 10.1080/00222933.2023.2186809, URL: http://dx.doi.org/10.6084/m9.figshare.22362999.v1

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urn:lsid:plazi.org:pub:3C4588028665487B125DFF885254E920

Cites
Publication: 10.1093/bioinformatics/bti263 (DOI)
Publication: 10.1093/nar/gks400 (DOI)
Publication: 10.1038/s41598-018-36132-6 (DOI)
Publication: 10.1016/j.ocecoaman.2012.03.007 (DOI)
Publication: 10.1093/nar/27.2.573 (DOI)
Publication: 10.1016/j.ympev.2012.08.023 (DOI)
Publication: 10.1093/bioinformatics/btp348 (DOI)
Publication: 10.1093/molbev/msaa297 (DOI)
Publication: 10.1080/23802359.2021.1899865 (DOI)
Publication: 10.1093/nar/gkz833 (DOI)
Publication: 10.1644/13-MAMM-A-265 (DOI)
Publication: 10.1186/s40555-015-0127-6 (DOI)
Publication: 10.1007/s11692-017-9428-5 (DOI)
Publication: 10.1093/nar/gkr1131 (DOI)
Publication: 10.1590/S0073-47212008000400009 (DOI)
Publication: 10.1093/bioinformatics/btv372 (DOI)
Publication: 10.1007/s11033-009-9641-0 (DOI)
Publication: 10.1093/molbev/msy096 (DOI)
Publication: 10.1007/s11033-019-05165-z (DOI)
Publication: 10.1093/sysbio/syx047 (DOI)
Publication: 10.21105/joss.00905 (DOI)
Publication: 10.1080/23802359.2017.1372723 (DOI)
Publication: 10.2307/1383304 (DOI)
Publication: 10.1371/journal.pone.0193984 (DOI)
Publication: 10.1007/s10661-012- (DOI)
Publication: 10.1111/mam.12098 (DOI)
Publication: 10.21203/rs.3.rs-817307/v1 (DOI)
Publication: 10.1186/s12864-016-3054-y (DOI)
Publication: 10.1016/S0378-1119(97)00404-6 (DOI)
Publication: 10.1002/0471250953.bi0313s48 (DOI)
Publication: 10.3390/genes13010125 (DOI)
Publication: 10.2144/00286ir01 (DOI)
Publication: 10.1093/bioinformatics/bti054 (DOI)
Publication: 10.3109/19401736.2015.1007363 (DOI)
Publication: 10.1016/j.ympev.2015.02.009 (DOI)
Publication: 10.1093/jhered/ess001 (DOI)
Publication: 10.1016/j.gene.2021.145868 (DOI)
Publication: 10.1186/1745-6150-4-20 (DOI)
Publication: 10.3389/fgene.2014.00109 (DOI)
Publication: 10.1016/j.gene.2006.12.040 (DOI)
Publication: 10.1186/1471-2148-11-92 (DOI)
Publication: 10.1016/j.gecco.2020.e01344 (DOI)
Has part
Figure: 10.5281/zenodo.7799806 (DOI)
Dataset: http://table.plazi.org/id/1CAA11E48663487D12FDFF06518AE985 (URL)
Figure: 10.5281/zenodo.7799808 (DOI)
Figure: 10.5281/zenodo.7799810 (DOI)
Figure: 10.5281/zenodo.7799812 (DOI)
Figure: 10.5281/zenodo.7799814 (DOI)
Figure: 10.5281/zenodo.7799816 (DOI)

References

  • Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 21:2104-2105. doi:10.1093/bioinformatics/bti263
  • Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, De Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, et al. 2012. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 40(W1): W597-W603. doi:10.1093/nar/gks400.
  • Avise JC. 2000. Phylogeography: the history and formation of species. Cambridge, MA: Harvard university press.
  • Baeza JA. 2018. The complete mitochondrial genome of the Caribbean spiny lobster Panulirus argus. Sci Rep. 8:17690. doi:10.1038/s41598-018-36132-6
  • Barbieri F, Machado R, Zappes CA, de Oliveira LR. 2012. Interactions between the Neotropical otter (Lontra longicaudis) and gillnet fishery in the southern Brazilian coast. Ocean Coast Manag. 63:16-23. doi:10.1016/j.ocecoaman.2012.03.007.
  • Bellaousov S, Reuter JS, Seetin MG, Mathews DH. 2013. RNAstructure: web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. 41:W471-W474. doi:10.1093/ nar/gkt290.
  • Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580. doi:10.1093/nar/27.2.573.
  • Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69:313-319. doi:10.1016/j.ympev.2012.08.023
  • Bikandi J, San Millan R, Rementeria A, Garaizar J. 2004. In silico analysis of complete bacterial genomes: PCR, AFLP-PCR, and endonuclease restriction. Bioinformatics. 20:798-799. doi:10. 1093/bioinformatics/btg491.
  • Brandt AP. 2004. Dieta e Uso do Habitat por Lontra longicaudis (Carnivora: Mustelidae) no Parque Estadual de Itapua , Viamao, RS. Porto Alegre, Rio Grande do Sul, Brazil: Curso de Pos-graduacao ao em Ecologia - Universidade Federal do Rio Grande do Sul, Porto Alegre.
  • Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 25:1972-1973. doi:10.1093/bioin formatics/btp348
  • Chak ST, Baeza JA, Barden P, Koichiro T. 2021. Eusociality shapes convergent patterns of molecular evolution across mitochondrial genomes of snapping shrimps. Mol Biol Evol. 38:1372-1383. doi:10.1093/molbev/msaa297.
  • Chehebar C. 1990. Action plan for Latin American Otters. In: Foster-Turley P, Macdonald S, Mason C, editors. 'Otters. An action plan for their conservation. 1st ed. Chapter: 12. Kelvyn Press, Inc., Broadview, Illinois, United States of America: IUCN/SSC Otter Specialist Editors; p. 64-73.
  • Chemes SB, Giraudo AR, Gil G. 2010. Dieta de Lontra longicaudis (Carnivora, Mustelidae) en el Parque Nacional el Rey (Salta, Argentina) y su comparacion con otras poblaciones de la cuenca del Parana. Mastozool Neotrop. 17:19-29.
  • Cucini C, Leo C, Iannotti N, Boschi S, Brunetti C, Pons J, Fanciulli PP, Frati F, Carapelli A, Nardi F. 2021. EZmito: a simple and fast tool for multiple mitogenome analyses. Mitochondrial DNA Part B. 6:1101-1109. doi:10.1080/23802359.2021.1899865
  • Donath A, Juhling F, Al-Arab M, Bernhart SH, Reinhardt F, Stadler PF, Middendorf M, Bernt M. 2019. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Res. 47(20):10543-10552. doi:10.1093/nar/gkz833.
  • Dunstone N, Strachan R. 1988. Status and distribution of otters in the Amboro National Park, Bolivia. IUCN Otter Spec Group Bull. 3:24-33.
  • Gallo-Reynoso JP. 1997. Situacion y distribucion de las nutrias en Mexico, con enfasis en Lontra longicaudis annectens Major, 1987. Rev Mex Mastozool. 2:10-32.
  • Gallo-Reynoso JP, Ramos-Rosas NN, Rangel-Aguilar O. 2008. Aquatic bird predation by neotropical river otter (Lontra longicaudis annectens), at Rio Yaqui, Sonora, Mexico. Rev Mex Bioodiv. 79:275-279.
  • Gomez JJ, Tunez JI, Fracassi N, Cassini MH. 2014. Habitat suitability and anthropogenic correlates of Neotropical river otter (Lontra longicaudis) distribution. J Mammal. 95:824-833. doi:10.1644/13- MAMM-A-265.
  • Gori M, Carpaneto GM, Ottino P. 2003. Spatial distribution and diet of the Neotropical otter Lontra longicaudis in the Ibera Lake (northern Argentina). Acta Theriol. 48:495-504. doi:10.1007/ BF03192495.
  • Hernandez-Romero PC, Guerrero JA, Valdespino C. 2015. Morphological variability of the cranium of Lontra longicaudis (Carnivora: Mustelidae): a morphometric and geographic analysis. Zool Stud. 54:1-12. doi:10.1186/s40555-015-0127-6.
  • Hernandez-Romero PC, Gutierrez-Rodriguez C, Valdespino C, Prieto-Torres DA. 2018. The role of geographical and ecological factors on population divergence of the Neotropical otter Lontra longicaudis (Carnivora, Mustelidae). Evol Biol. 45:37-55. doi:10.1007/s11692-017-9428-5.
  • Jang KH, Hwang UW. 2016. Complete mitochondrial genome of Korean yellow-throated marten, Martes flavigula (Carnivora, Mustelidae). Mitochondrial DNA Part A. 27:1785-1786.
  • Jang KH, Ryu SH, Hwang UW. 2009. Mitochondrial genome of the eurasian otter Lutra lutra (Mammalia, Carnivora, Mustelidae). J Genet Genomics. 31:19-27.
  • Jeon MG, Kim HR, Min JH, Kim HJ, Park YC. 2017. Complete mitochondrial genome of the Asian badger Meles leucurus (Mustelidae) from Korea. Mitochondrial DNA Part B. 2:556-557. doi:10. 1080/23802359.2017.1365648.
  • Jin JJ, Yu WB, Yang JB, Song Y, DePamphilis CW, Yi TS, Li DZ. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21:1-31. doi:10.1186/ s13059-020-02154-5.
  • Juhling F, Putz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF. 2012. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res. 40:2833-2845. doi:10.1093/nar/gkr1131.
  • Kasper CB, Bastazini VAG, Salvi J, Grillo HCZ. 2008. Trophic ecology and the use of shelters and latrines by the Neotropical otter (Lontra longicaudis) in the Taquari Valley, Southern Brazil. Iheringia Serie Zoologia. 98:469-474. doi:10.1590/S0073-47212008000400009.
  • Kerpedjiev P, Hammer S, Hofacker IL. 2015. Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams. Bioinformatics. 31(20):3377-3379. doi:10.1093/bioinfor matics/btv372.
  • Ki JS, Hwang DS, Park TJ, Han SH, Lee JS. 2010. A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae). Mol Biol Rep. 37 (4):1943-1955. doi:10.1007/s11033-009-9641-0.
  • Kruuk H. 2006. Otters: ecology, behaviour and conservation. Great Britain: Oxford University Press.
  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K, Battistuzzi FU. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35:1547-1549. doi:10.1093/molbev/ msy096.
  • Lariviere S. 1999. Lontra longicaudis. Mamm Species. 609:1-5.
  • Latorre-Cardenas MC, Gutierrez-Rodriguez C, Lance SL. 2020. Isolation and characterization of 13 microsatellite loci for the Neotropical otter, Lontra longicaudis, by next generation sequencing. Mol Biol Rep. 47:731-736. doi:10.1007/s11033-019-05165-z.
  • Law CJ, Slater GJ, Mehta RS. 2018. Lineage diversity and size disparity in Musteloidea: testing patterns of adaptive radiation using molecular and fossil-based methods. Syst Biol. 67:127-144. doi:10.1093/sysbio/syx047.
  • Lee BD. 2018. Python implementation of codon adaptation index. J Open Source Software. 3:905. doi:10.21105/joss.00905.
  • Lim SJ, Kim HR, Cho JY, Park YC. 2017. Complete mitochondrial genome of the least weasel Mustela nivalis (Mustelidae) in Korea. Mitochondrial DNA Part B. 2:740-741. doi:10.1080/23802359.2017. 1372723.
  • Lopez-Cuamatzi IL, Ortega J, Baeza JA. 2021. The complete mitochondrial genome of the 'Zacatuche̍ Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico. Mol Biol Rep. 49:1141-1149.
  • Melquist WE, Hornocker MG. 1983. Ecology of river otters in west central Idaho. Wildl Monogr. 83:1-60.
  • Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32:268-274. doi:10. 1093/molbev/msu300.
  • Nowak RM. 1999. Walker̍s mammals of the world. Vol. I. Baltimore (MD): Johns Hopkins University.
  • Pardini R, Trajano E, Lee BD. 1999. Use of shelters by the neotropical river otter (Lontra longicaudis) in an Atlantic forest stream, southeastern Brazil. J Mammal. 80:600-610. doi:10.2307/1383304.
  • Pimenta NC, Antunes AP, Barnett AA, Macedo VW, Shepard GH Jr. 2018. Differential resilience of Amazonian otters along the Rio Negro in the aftermath of the 20th century international fur trade. PLoS ONE. 13(3):e0193984. doi:10.1371/journal.pone.0193984.
  • Ramos-Rosas NN, Valdespino C, Garcia-Hernandez J, Gallo-Reynoso JP, Olguin EJ. 2013. Heavy metals in the habitat and throughout the food chain of the Neotropical otter, Lontra longicaudis, in protected Mexican wetlands. Environ Monit Assess. 185:1163-1173. doi:10.1007/s10661-012- 2623-z.
  • Rheingantz ML, Oliveira-Santos LG, Waldemarin HF, Caramaschi EP. 2012. Are otters generalists or do they prefer larger, slower prey? Feeding flexibility of the Neotropical Otter Lontra longicaudis in the Atlantic Forest. IUCN Otter Specialist Group Bull. 29(2):80-94.
  • Rheingantz LM, Santiago-Plata VM, Trinca CS. 2017. The Neotropical otter Lontra longicaudis: a comprehensive update on the current knowledge and conservation status of this semiaquatic carnivore. Mammal Rev. 47:291-305. doi:10.1111/mam.12098.
  • Rheingantz ML, Trinca CS 2015. Lontra longicaudis. The IUCN Red List of Threatened Species. e. T12304A21937379.
  • Rheingantz M, Valenzuela A, Botero-Botero A, de Thoisy B, Trujillo F, Gonzalez I, Gallo-Reynoso JP, Marmonet M, Hernandez-Romero PC, Rosas-Ribeiro PF, et al. 2018. Neotropical otter (Lontra longicaudis). In: Duplaix N, Savage M, editors. The global otter conservation strategy. Salem (OR): IUCN/SSC Otter Specialist Group; p. 82-89.
  • Rivera LMM, Rodriguez-Aguilar B, Martinez-Rivera L, Muniz-Valencia R, Mercado-Silva N, Iniguez-Davalos L, Peregrina-Lucano AA. 2022. Study of feces of neotropical otters (Lontra longicaudis) in the Ayuquila-Armeria basin, Mexico as biomonitors of the spatiotemporal distribution of pesticides. doi:10.21203/rs.3.rs-817307/v1.
  • Satoh TP, Miya M, Mabuchi K, Nishida M. 2016. Structure and variation of the mitochondrial genome of fishes. BMC Genomics. 17(1):1-20. doi:10.1186/s12864-016-3054-y.
  • Sbis`a E, Tanzariello F, Reyes A, Pesole G, Saccone C. 1997. Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene. 205:125-140. doi:10.1016/S0378-1119(97)00404-6.
  • Sievers F, Higgins DG. 2014. Clustal omega. Curr Protoc Bioinf. 48:3-13. doi:10.1002/0471250953. bi0313s48
  • Skorupski J. 2020. Fifty years of research on European mink Mustela lutreola L., 1761 genetics: where are we now in studies on one of the most endangered mammals? Genes. 11:1332. doi:10.3390/ genes11111332.
  • Skorupski J. 2022. Characterisation of the complete mitochondrial genome of critically endangered Mustela lutreola (Carnivora: Mustelidae) and its phylogenetic and conservation implications. Genes. 13(1):125. doi:10.3390/genes13010125.
  • Stothard P. 2000. The sequence manipulation suite: javaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques. 28:1102-1104. doi:10.2144/00286ir01.
  • Stothard P, Wishart DS. 2004. Circular genome visualization and exploration using CGView. Bioinformatics. 21:537-539. doi:10.1093/bioinformatics/bti054.
  • Sun WL, Wang SJ, Wan Z, Liu HL, Zhong W, Yang YH, Li GY. 2016. The complete mitochondrial genome sequence of Neovison vison (Carnivora: Mustelidae). Mitochondrial DNA Part A. 27:1840-1841. doi:10.3109/19401736.2015.1007363.
  • Tan MH, Gan HM, Schultz MB, Austin CM. 2015. MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Mol Phylogenet Evol. 85:180-188. doi:10.1016/j. ympev.2015.02.009.
  • Trinca CS, De Thoisy B, Rosas FCW, Waldemarin HF, Koepfli KP, Vianna JA, Eizirik E. 2012. Phylogeography and demographic history of the Neotropical otter (Lontra longicaudis). J Heredity. 103:479-492. doi:10.1093/jhered/ess001.
  • Vivas-Toro I, Ortega J, Baeza JA. 2021. The complete mitochondrial genome of the Honduran white bat Ectophylla alba (Allen 1982) (Chiroptera: Phyllostomidae). Gene. 802:145868. doi:10.1016/j. gene.2021.145868.
  • Wang DP, Wan HL, Zhang S, Yu J. 2009. γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biol Direct. 4:1-18. doi:10.1186/1745-6150-4-20
  • Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. 2010. KaKs_Calculator 2.0: a toolkit incorporating gammaseries methods and sliding window strategies. Genomics Proteomics Bioinf. 8:77-80. doi:10.1016/ S1672-0229(10)60008-3.
  • Watanabe Y, Suematsu T, Ohtsuki T. 2014. Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors. Front Genet. 5:109. doi:10.3389/fgene. 2014.00109
  • Wilson DE, Reeder DM. 2005. Mammal species of the world. A taxonomic and geographic reference. 3rd ed. Baltimore (MD): Johns Hopkins University Press; p. 2142.
  • Yonezawa T, Nikaido M, Kohno N, Fukumoto Y, Okada N, Hasegawa M. 2007. Molecular phylogenetic study on the origin and evolution of Mustelidae. Gene. 396:1-12. doi:10.1016/j.gene.2006.12.040.
  • Yu L, Peng D, Liu J, Luan P, Liang L, Lee H, Lee M, Ryder OA, Zhang Y. 2011. On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes. BMC Evol Biol. 11:92. doi:10.1186/1471-2148-11-92.
  • Zhang C, Zhu R, Sui X, Chen K, Li B, Chen Y. 2020. Ecological use of vertebrate surrogate species in ecosystem conservation. Global Ecol Conserv. 24:e01344. doi:10.1016/j.gecco.2020.e01344