Primers for amplification and sequencing the complete mitochondrial genome in Octodontoid rodents
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TECHNICAL NOTE
Primers for amplification and sequencing the complete mitochondrial genome in Octodontoid rodents Ivanna H. Tomasco • Enrique P. Lessa
Received: 23 August 2013 / Accepted: 24 March 2014 Ó Springer Science+Business Media Dordrecht 2014
Abstract The mitochondrial genome is useful for research in conservation genetics. Complete sequences have been reported for hundreds of mammalian species, but the Neotropical fauna is underrepresented. We report 65 primers to amplify and sequence the complete mitochondrial genomes of Octodontoid rodents, of which more than one-fifth are endangered species. Keywords
Mitochondrial markers Octodontoid rodents
Mitochondrial genes have been widely used in phylogenetic and population studies. Properties of mitochondrial genome, i.e.: haploidity and maternal transmission, extensive intraspecific variation and usual absence of intermolecular recombination, make it useful for research in conservation genetics. The mitochondrial genome has been completely sequenced and reported for hundreds of mammal species. Despite its high diversity, the South American fauna is underrepresented (\10 %). Caviomorph rodents are particularly interesting for evolutionary biologists because they are phylogenetically and adaptively divergent from other rodents. At the molecular level, conspicuous examples are their divergent insulin gene (Opazo et al. 2005) and some mitochondrial genes under positive
Electronic supplementary material The online version of this article (doi:10.1007/s12686-014-0163-2) contains supplementary material, which is available to authorized users. I. H. Tomasco (&) E. P. Lessa Laboratorio de Evolucio´n, Departamento de Ecologı´a y Evolucio´n, Facultad de Ciencias, Universidad de la Repu´blica, Igua´ 4225, 11400 Montevideo, Uruguay e-mail: [email protected] E. P. Lessa e-mail: [email protected]
selection in subterranean genera (Tomasco and Lessa 2011). Octodontoidea is the most diverse caviomorph superfamily, with 193 species (e.g.: Upham and Patterson 2012). Following the IUCN Red List of Threatened species (IUCN 2013.1), more than 22 % of the octodontoids face a high risk of global extinction (7.3 % listed as Critically Endangered, 8.8 % Endangered and 6.2 % Vulnerable) and 29.5 % of the species are Data Deficient. The 60 subterranean tuco–tuco species (Ctenomys) were considered one of the most rapidly speciating mammalian lineages (Reig et al. 1990), but 25 % are endangered and 40 % categorized as ‘‘Data Deficient’’. 65 primers were designed to amplify overlapping fragments of the mtDNA genome of Octodontoid rodents (Table 1). Initial primers were designed using conserved mtDNA regions of two hystricognath rodents (Cavia porcellus (NC_000884), Thryonomys swinderianus (NC_002658)) to amplify 1–2.5 Kb length fragments which were sequenced from both ends. Based on these sequences, specific primers were designed to complete internal sequencing (see Supplemetary material S1). Additional primers used were: Tuco06, Tuco07, Tuco14A (Wlasiuk et al. 2003), TucoPro (Tom
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