In this work, we present for the first time the mitochondrial genome of a paradoxical frog (Pseudis tocantins). This genome is 15.56 kb, excluding the control region, and is similar in gene content to other hylid mitogenomes. Maximum likelihood analysis, using the mitogenomes of several anurans, indicated P. tocantins as closely related to other hylid species

Gatto, Kaleb Pretto

Lourenço, Luciana Bolsoni

Smith, Jeramiah J.

English

University of Kentucky

University of KentuckyUKnowledgeBiology Faculty Publications Biology10-26-2018The Mitochondrial Genome of the EndemicBrazilian Paradoxial Frog Pseudis tocantins (Hylidae)Kaleb Pretto GattoUniversity of Campinas, BrazilJeramiah J. SmithUniversity of Kentucky, jeramiah.smith@uky.eduLuciana Bolsoni LourençoUniversity of Campinas, BrazilRight click to open a feedback form in a new tab to let us know how this document benefits you.Follow this and additional works at: https://uknowledge.uky.edu/biology_facpubPart of the Biology Commons, and the Genetics and Genomics CommonsThis Article is brought to you for free and open access by the Biology at UKnowledge. It has been accepted for inclusion in Biology Faculty Publicationsby an authorized administrator of UKnowledge. For more information, please contact UKnowledge@lsv.uky.edu.Repository CitationGatto, Kaleb Pretto; Smith, Jeramiah J.; and Lourenço, Luciana Bolsoni, "The Mitochondrial Genome of the Endemic BrazilianParadoxial Frog Pseudis tocantins (Hylidae)" (2018). Biology Faculty Publications. 160.https://uknowledge.uky.edu/biology_facpub/160The Mitochondrial Genome of the Endemic Brazilian Paradoxial Frog Pseudis tocantins (Hylidae)Notes/Citation InformationPublished in Mitochondrial DNA Part B, v. 3, no. 2, p. 1106-1107.© 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.This is an Open Access article distributed under the terms of the Creative Commons Attribution License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.Digital Object Identifier (DOI)https://doi.org/10.1080/23802359.2018.1508385This article is available at UKnowledge: https://uknowledge.uky.edu/biology_facpub/160Full Terms & Conditions of access and use can be found athttps://www.tandfonline.com/action/journalInformation?journalCode=tmdn20Mitochondrial DNA Part BResourcesISSN: (Print) 2380-2359 (Online) Journal homepage: https://www.tandfonline.com/loi/tmdn20The mitochondrial genome of the endemicBrazilian paradoxical frog Pseudis tocantins(Hylidae)Kaleb Pretto Gatto, Jeramiah J. Smith & Luciana Bolsoni LourençoTo cite this article: Kaleb Pretto Gatto, Jeramiah J. Smith & Luciana Bolsoni Lourenço (2018)The mitochondrial genome of the endemic Brazilian paradoxical frog Pseudis￿tocantins (Hylidae),Mitochondrial DNA Part B, 3:2, 1106-1107, DOI: 10.1080/23802359.2018.1508385To link to this article:  https://doi.org/10.1080/23802359.2018.1508385© 2018 The Author(s). Published by InformaUK Limited, trading as Taylor & FrancisGroup.Published online: 26 Oct 2018.Submit your article to this journal Article views: 72View Crossmark dataMITOGENOME ANNOUNCEMENTThe mitochondrial genome of the endemic Brazilian paradoxical frog Pseudistocantins (Hylidae)Kaleb Pretto Gattoa, Jeramiah J. Smithb and Luciana Bolsoni LourençoaaLaboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute of Biology, University of Campinas,Campinas, Brazil; bDepartment of Biology, College of Arts and Sciences, University of Kentucky, Lexington, USAABSTRACTIn this work, we present for the first time the mitochondrial genome of a paradoxical frog (Pseudistocantins). This genome is 15.56 kb, excluding the control region, and is similar in gene content toother hylid mitogenomes. Maximum likelihood analysis, using the mitogenomes of several anurans,indicated P. tocantins as closely related to other hylid species.ARTICLE HISTORYReceived 16 July 2018Accepted 29 July 2018KEYWORDSMitochondrion; mtDNA;Anura; next-generationsequencing;paradoxical frogThe paradoxical frog Pseudis tocantins Caramaschi and Cruz1998 is endemic to Brazilian savannas associated withAraguaia and Tocantins river basins (Frost 2018). Interestingfeatures of the paradoxical frogs are related to (1) theirextended larval period that results in tadpoles attaining bodysizes that are substantially larger than metamorphosed adults(Shaw 1802; Garda et al. 2010; Santana et al. 2016), and (2)the study of sex chromosome differentiation, as P. tocantinshas highly heteromorphic sex chromosomes (Busin et al.2008; Gatto et al. 2016). Here, we describe the completemitochondrial genome of P. tocantins.Total genomic DNA was isolated from the liver of a femaleP. tocantins collected from the type locality of this species(i.e. Porto Nacional, Tocantins state in Brazil – 1044038.600S4826009.200W), using a standard phenol:chloroform extractionprotocol (Sambrook et al. 1989). The remaining tissue isdeposited in the tissue collection of the Laboratory ofChromosome Studies of the University of Campinas, Brazil(LabEsC – UNICAMP) under the accession number SMRP190.15 and the specimen voucher is deposited at theamphibian collection of the Museu de Zoologia ProfessorAd~ao Jose Cardoso at the University of Campinas, Brazil,under the accession number ZUEC 22351. Permission for col-lecting the specimen was granted by SISBIO (process 45183)and Committee for Ethics in Animal Use of the University ofCampinas (CEUA/UNICAMP) (process 3419-1).A paired-end genomic library was prepared using NexteraDNA Flex Library Prep Kit (Illumina, EUA) and sequenced onan Illumina HiSeq X Ten (Hudson-Alpha Institute forBiotechnology, Alabama, USA). We detected k-mers (k¼ 31)occurring at high frequencies among genomic reads usingRepARK script (Koch et al. 2014) and default parameters.These high-frequency k-mers were then assembled by Velvet(Zerbino and Birney 2008) using default parameters. Genomeannotation was performed using MITOS (Bernt et al. 2013).The mitochondrial genome contig was compared with avail-able hylid mitochondrial genomes using BLAST (Altschulet al. 1990). The complete mitochondrial genome ofP. tocantins, excluding control region, was used in a phylo-genetic analysis in comparison with other 13 anurans species.Sequences were aligned using Muscle (Edgar 2004) and usedfor a Maximum likelihood analysis in RAxML v.0.4.1b(Stamakis 2014), under the GTRþG evolutionary model.The assembled mitogenome of P. tocantins (GenBankaccession number MH571152) spanned 15.56 kb, with a GCcontent of 43.16%. This genome is similar to those of otherhylids in size, gene content, and arrangement, with an aver-age nucleotide similarity of 70% when compared to six spe-cies from HylaþDryophytes. There are 13 protein-codinggenes, 22 tRNA genes, and 2 rRNA genes. These genes arecoded in the heavy strand, except for eight tRNA genes(tRNA-Pro, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr,tRNA-Ser, tRNA-Glu) and one protein-coding gene (ND6).The resulting phylogenetic tree placed P. tocantins as thesister taxon of all extant hylid species analyzed in this paper(Figure 1). This result agrees with the large-scale phylogen-etic inferences published thus far, as they place Pseudis as amember of the Hylidae family (Faivovich et al. 2005; Wienset al. 2010; Pyron and Wiens 2011; Duellman et al. 2016).CONTACT Kaleb Pretto Gatto kaleb.gatto@gmail.com Laboratory of Chromosome Studies, Department of Structural and Functional Biology, Institute ofBiology University of Campinas, Campinas, Brazil 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use,distribution, and reproduction in any medium, provided the original work is properly cited.MITOCHONDRIAL DNA PART B2018, VOL. 3, NO. 2, 1106–1107https://doi.org/10.1080/23802359.2018.1508385Disclosure statementNo potential conflict of interest was reported by authors.FundingThis work was supported by S~ao Paulo Research Foundation (FAPESP)(#2014/23542-6). PhD studentships were provided by National Councilfor Scientific and Technological Development (CNPq) (140814/2015-9)and Coordination for the Improvement of Higher Education Personnel(CAPES) (PDSE 99999.006901/2015-08).ReferencesAltschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic localalignment search tool. J Mol Biol. 215:403–410.Bernt M, Donath A, J€uhling F, Externbrink F, Florentz C, Fritzsch G, P€utz J,Middendorf M, Stadler PF. 2013. MITOS: Improved de novo metazoanmitochondrial genome annotation. Mol Phylogenet Evol. 69:313–319.Busin CS, Andrade GV, Bertoldo J, Del Grande ML, Uetanabaro M, Recco-Pimentel SM. 2008. Cytogenetic analysis of four species of Pseudis(Anura, Hylidae), with the description of ZZ/ZW sex chromosomes inP. tocantins. Genetica. 133:119–127.Caramaschi U, Cruz CAG. 1998. Notas taxonômicas sobre Pseudis fuscaGarman e P. bolbodactyla A. Lutz, com a descriç~ao de uma novaespacie correlata (Anura, Pseudidae). Rev Bras Zool. 15:929–944.Duellman WE, Marion AB, Hedges SB. 2016. Phylogenetics, classification,and biogeography of the treefrogs (Amphibia: Anura: Arboranae).Zootaxa. 4104:1–109.Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accur-acy and high throughput. Nucleic Acids Res. 32: 1792–1797.Faivovich J, Haddad CFB, Garcia PCA, Frost DR, Campbell JA, WheelerWC. 2005. Systematic review of the frog family Hylidae, with specialreference to Hylinae: phylogenetic analysis and taxonomic revision.Bull Am Museum Nat Hist. 294:1–240.Frost DR. 2018. Amphibian Species of the World 6.0: An OnlineReference. New York: American Museum of Natural History; [accessed2018 Jul 06]. http://research.amnh.org/vz/herpetology/amphibia/.Garda AA, Santana DJ, S~ao-Pedro V. d A. 2010. Taxonomic characteriza-tion of paradoxical frogs (Anura, Hylidae, Pseudae): geographic distri-bution, external morphology, and morphometry. Zootaxa. 2666:1–28.Gatto KP, Busin CS, Lourenço LB. 2016. Unraveling the sex chromosomeheteromorphism of the paradoxical frog Pseudis tocantins. PLoS One.11:e0156176.Koch P, Platzer M, Downie BR. 2014. RepARK – de novo creation ofrepeat libraries from whole-genome NGS reads. Nucleic Acids Res.42:e80.Pyron RA, Wiens JJ. 2011. A large-scale phylogeny of Amphibia includingover 2800 species, and a revised classification of extant frogs, sala-manders, and caecilians. Mol Phylogenet Evol. 61:543–583.Sambrook J, Fritschi EF, Maniats T. 1989. Molecular cloning: a laboratorymanual. 2nd ed. New York (NY): Cold Spring Harbor Laboratory Press.Santana DJ, Magalh~aes F. de M, S~ao-Pedro V. de A, Mângia S, Amado TF,Garda AA. 2016. Calls and tadpoles of the species of Pseudis (Anura,Hylidae, Pseudae). Herpetol J. 26:139–148.Shaw G. 1802. General zoology or systematic natural history. Volume III,Part 1. Amphibia. London (UK): Thomas Davison.Stamakis A. 2014. RAxML version 8: a tool for phylogenetic analysis andpost-analysis of large phylogenies. Bioinformatics. 30: 1312–1313.Sun Q, Xie Y, Zhao W, Liu P. 2017. Sequencing and analysis of the com-plete mitochondrial genome of Hyla ussuriensis (Anura: Hylidae).Mitochondr DNA part A. 28: 328–329.Wang X, Wang Y, Yue B, Zhang X, Liu S. 2017. The complete mitochon-drial genome of the Bufo tibetanus (Anura: Bufonidae). MitochondrDNA. 24: 186–188.Wiens JJ, Kuczynski CA, Hua X, Moen DS. 2010. An expanded phylogenyof treefrogs (Hylidae) based on nuclear and mitochondrial sequencedata. Mol Phylogenet Evol. 55:871–882.Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res. 18:821–829.Figure 1. Phylogenetic inference obtained using maximum likelihood based on mitochondrial genomes, excluding control region, of the anuran species Dryophytesjaponicus, D. ussuriensis, (as Hyla ussuriensis in Sun et al. 2017), D. suweonensis (as H. suweonensis in Lee et al. 2017), Hyla chinensis, H. annectans, Hyla tsinlingensis,Pseudis tocantins, Bufo gargarizans, B. tibetanus (as in Wang et al. 2013), stejnegeri, B. japonicus, Telmatobufo australis, Microhyla okinavensis and Lithobates catesbeia-nus. M. okinavensis and L. catesbeianus were used as outgroups. The phylogenetic inference was constructed under GTRþG evolutionary model. Bootstrap analysiswas performed using 1000 pseudoreplicates for node support (numbers at the nodes).MITOCHONDRIAL DNA PART B 1107

The Mitochondrial Genome of the Endemic Brazilian Paradoxial Frog \u3cem\u3ePseudis tocantins\u3c/em\u3e (Hylidae)

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The Mitochondrial Genome of the Endemic Brazilian Paradoxial Frog \u3cem\u3ePseudis tocantins\u3c/em\u3e (Hylidae)

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