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Mitochondrial DNA, Early Online: 1–3! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.982563

MITOGENOME ANNOUNCEMENT

Complete mitochondrial genome sequence of Grundulus bogotensis(Humboldt, 1821).

Juan P. Isaza1, Juan F. Alzate1, and Javier A. Maldonado-Ocampo2

1Facultad de Medicina, Centro Nacional de Secuenciacion Genomica, Universidad de Antioquia, Medellin, Colombia and 2Laboratorio de Ictiologıa,

Unidad de Ecologıa y Sistematica (UNESIS), Departamento de Biologıa, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogota, Colombia

Abstract

The Grundulus bogotensis is an Endangered fish in Colombia. In this study, we report thecomplete mitochondrial DNA sequences of G. bogotensis. The entire genome comprised 17.123bases and a GC content of 39.84%. The mitogenome sequence of G. bogotensis wouldcontribute to better understand population genetics, and evolution of this lineage. Moleculewas deposited at the GenBank database under the accession number KM677190.

Keywords

Characidae, Characiformes, Colombia,Gymnocharacinae, mitogenome

History

Received 5 October 2014Accepted 18 October 2014Published online 17 November 2014

Grundulus is a genus belonging to the Characidae family, orderCharaciformes. Grundulus was one of the 80 genera considered asincertae sedis in Characidae by Lima et al. (2003). Recentsystematics studies of Characidae include Grundulus as part ofthe subfamily Gymnocharacinae as sister of Coptobrycon(Mirande 2009, 2010). Grundulus bogotensis an endemic speciesto the highlands in the Altiplano Cundiboyacense in Colombiawas describe by Humboldt in 1821, from the wetland system thatwas present in what today is place the capital of Colombia,Bogota. In some places, this species was an important food sourcefor local people and is still exploited by some communities(Rivera-Rondon et al., 2008). Nonetheless, as a consequence ofanthropogenic habitat transformation, G. bogotensis was includedin the Red Book of Freshwater Fishes of Colombia, under thecategory of ‘‘Near Threatened’’ (Alvarez-Leon et al., 2002) andupdated in 2012 under the category of ‘‘Least Concern’’ (Alvarez-Leon et al., 2012).

Specimens of G. bogotensis were captured in the Rio Ubate.One biopsy of skeletal muscle was taken from one specimen andgenomic DNA extracted using a commercial column method. Awhole genome shotgun DNA library was constructed andsequenced using the 454 GS FLX (+) platform (ROCHE,Switzerland). Read assembly was carried out using Newbler

v2.6 (Margulies et al., 2005) and contigs carrying mitochondrialgenes were identified using BLAST package (Camacho et al.,2008) against mitochondrial sequences of other Characidaefishes. Only one contig carrying mitochondrial genetic informa-tion was found and it showed an average read depth of 14.4X.PCR amplification a capillary sequencing allowed confirmingthe circularity and ambiguities. At the end, the completemitogenome of 17.123 bases and a GC content of 39.84% wasannotated using as reference the mitochondrial genome ofAstyanax mexicanus (GenBank AP011982) with ARTEMISpackage (Rutherford et al., 2000) and MITOS prediction webserver (Bernt et al., 2013). Thirteen protein-coding genes andtwo ribosomal RNAs were annotated as follows: cox1, cox2,atp8, atp6, cox3, nd3, nd4l, nd4, nd5, nd6, cytb, nd1, nd2, rrnLand rrnS. Twenty-two mitochondrial tRNAs were annotated:trnS2 (TGA), trnD (GTC), trnK (TTT), trnG (TCC), trnR(TCG), trnH (GTG), trnS1 (GCT), trnL1 (TAG), trnE (TTC),trnT (TGT), trnP (TGG), trnF (GAA), trnV (TAC), trnL2(TAA), trnI (GAT), trnQ (TTG), trnM (CAT), trnW (TCA), trnA(TGC), trnN (GTT), trnC (GCA), and trnY (GTA). PutativeD-loop region is located between genes trnP and trnF(Figure 1). The mitochondrial genomes of Grundulus bogotensisand Astyanax mexicanus present complete synteny.

Correspondence: Javier A. Maldonado-Ocampo, Laboratorio de Ictiologıa 108B, Edf. 53, Pontificia Universidad Javeriana, Carrera 7 # 43-82, BogotaD.C., Colombia. Tel: +571-3208320 ext 4071. E-mail: maldonadoj@javeriana.edu.co

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Acknowledgements

Edgar Herrera and Saul Prada Pedreros for their assistance during FieldWork.

Declaration of interest

This research was funded by the Division of Research, PontificiaUniversidad Javeriana (Project 5447), and Instituto Alexander vonHumboldt (Agreement 005, 2013) to Javier A. Maldonado O. Theauthors report no conflict of interest and also state that they areresponsible for content and writing of the paper.

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Figure 1. Mitochondrial genome graphical representation of Grundulus bogotensis. White rectangles represent the coding sequences. Small rectanglesdepict tRNA genes. Dark gray rectangles depict ribosomal RNA genes. Inside, histogram represents the GC content.

2 J. P. Isaza et al. Mitochondrial DNA, Early Online: 1–3

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DOI: 10.3109/19401736.2014.982563 Mitochondrial genome of G. bogotensis 3

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