http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.984170
MITOGENOME ANNOUNCEMENT
Complete mitogenome of the Neotropical fish Brycon henni, Eigenmann 1913 (Characiformes, Bryconidae) Ricardo M. Landı´nez-Garcı´a1, Juan F. Alzate2, and Edna J. Ma´rquez1 Facultad de Ciencias, Universidad Nacional de Colombia, Medellı´n, Colombia and 2Centro Nacional de Secuenciacio´n Geno´mica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellı´n, Colombia
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/06/15 For personal use only.
1
Abstract
Keywords
Brycon henni (Characiformes, Bryconidae) is a trans-Andean omnivorous fish considered as promising species in aquaculture of temperate zones. In this work we report for first time the complete mitochondrial genome of B. henni. This mitogenome spans 16,885 bp and encodes 13 proteins, 22 tRNAs and 2 ribosomal RNAs. Additionally, the synteny is conserved with others species of the order Characiformes.
Freshwater fish, Illumina sequencing, mitogenome, Otophisy
The phylogenetics and taxonomy of the family Bryconidae and its relationships with the order Characiformes have been subject of several controversies (Nakatani et al., 2011; Oliveira et al., 2011). A study about the systematic and historical biogeography of the Bryconidae (Abe et al., 2014) show that the cis- and trans-Andean members of Brycon are not monophyletic and the relationship among cis-Andean species of this clade remain unresolved. Although the mitogenome of Brycon orbignyanus was recently published (Siqueira et al., 2014), a wider sampling of taxas and individuals are required to improve our understanding of the relationships between the families Bryconidae and Characidae. Thus, this work reports the complete mitochondrial genome of B. henni, an trans-Andean omnivorous fish considered as promising in aquaculture of temperate zones (Lenis et al., 2009). In this work, one specimen of B. henni was collected in Cauca river (Colombia) and a sample from skeletal muscle tissue was used for genomic DNA isolation. Sequencing process was performed with Illumina Miseq platform using the whole genome shotgun strategy and 250 bases paired-end reads. Obtained reads were screened for the presence of mitochondrial sequences using a custom database of mitochondrial genomes of related species and the algorithm BLASTN (Bethesda, MD) (Altschul et al., 1997). Filtered reads were then assembled with the NEWBLER package v2.9
History Received 29 October 2014 Accepted 1 November 2014 Published online 25 November 2014
(Branford, CT) (Margulies et al., 2005) and the obtained contig was further annotated using the softwares ARTEMIS v16.0.0 (Cambridge, UK) (Rutherford et al., 2000) and MITOS prediction server (Leipzig, Germany) (Bernt et al., 2013). Annotation conflicts were resolved using MITOFISH web server (Tokyo, Japan) (Iwasaki et al., 2013). The mitogenome of B. henni (GenBank Accession number KP027535) is 16,885 bp in length and the overall base composition is A: 29.65%, C: 28.36%, G: 16.19% and T: 25.77%. This mitogenome contains 13 coding sequences (CDS) related to the respiratory chain, 2 ribosomal RNA genes (rRNA), 22 transfer RNAs and a 1208 bp D-loop region (Figure 1). The CDS sequences correspond to the genes cox1, cox2, atp8, atp6, cox3, nad3, nad4l, nad4, nad5, nad6, cytb, nad1 and nad2. The CDS sequences (except nad6), D-loop and the rRNA genes mt-rnr1 and mt-rnr2 are in the same strand. The 22 tRNA genes distributed in both strands are: trnD(GTC), trnK(TTT), trnG(TCC), trnR(TCG), trnH(GTG), 2 trnS(GCT, TGA), 2 trnL(TAG, TAA), trnE(TTC), trnT(TGT), trnP(TGG), trnF(GAA), trnV(TAC), trnI(GAT), trnQ(TTG), trnM(CAT), trnW(TCA), trnA(TGC), trnN(GTT), trnC(GCA) and trnY(GTA). This mitogenome presents perfect synteny with others members of order Characiformes such as Brycon orbignyanus (Bryconidae), Astyanax mexicanus (Characidae), Curimatopsis evelynae (Curimatidae) and Prochilodus lineatus (Prochilodontidae).
Correspondence: Edna Ma´rquez, Facultad de Ciencias, Universidad Nacional de Colombia, Calle 59A No 63 – 20 Bloque 19 A Laboratorio 310, Medellı´n, Colombia. Tel: (57)(4) 4309072. Fax: (57)(4) 4309116. E-mail: [email protected], [email protected].
2
R. M. Landı´nez-Garcı´a et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Graphical map of the Brycon henni mitochondrial genome. The arrows represent the coding sequences. Small squares represent the tRNA genes. Solid and striped rectangles depict ribosomal RNA genes and D-loop region, respectively. In the center, a histogram represents the GC content.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/06/15 For personal use only.
Brycon henni 16,885 bp
Declaration of interest The author reports no conflict of interest. The authors alone are responsible for content and writing of the paper. This work was funded by the Universidad Nacional de Colombia, Sede Medellı´n and Empresas Pu´blicas de Medellı´n, Grant CT-2013002443 ‘‘Variacio´n genotı´pica y fenotı´pica de poblaciones de especies reo´filas presentes en el a´rea de influencia del proyecto hidroele´ctrico Ituango’’.
References Abe KT, Mariguela TC, Avelino GS, Foresti F, Oliveira C. (2014). Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna. BMC Evol Biol Biol 14:152–67. Altschul SF, Madden TL, Scha¨ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389–402. Bernt M, Donath A, Ju¨hling F, Externbrink F, Florentz C, Fritzsch G, Pu¨tz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial
genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Lenis GA, Restrepo LF, Rivera JC, Monsalve F, Cruz-Casallas PE. (2009). Reproduccio´n inducida y produccio´n de alevinos de sabaleta Brycon henni: Determinacio´n del tiempo de latencia utilizando extracto de hipo´fisis de carpa. Rev Colomb Ciencias Pecu 22:143–55. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, et al. (2005). Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376–80. Nakatani M, Miya M, Mabuchi K, Saitoh K, Nishida M. (2011). Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evol Biol 11:177–202. Oliveira C, Avelino GS, Abe KT, Mariguela TC, Benine RC, Ortı´ G, Vari RP, et al. (2011). Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling. BMC Evol Biol 11: 1–25. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B. (2000). Artemis: Sequence visualization and annotation. Bioinformatics 16:944–5. Siqueira F de F, Carmo AO do, Pimentel J da SM, Kalapothakis E. (2014). Complete mitochondrial genome sequence of Brycon orbignyanus (Characiformes, Bryconidae). Mitochondrial DNA. Available at: http://informahealthcare.com/doi/abs/10.3109/19401736. 2014.971298 (Accessed 28 October 2014).
MITOGENOME ANNOUNCEMENT
Complete mitogenome of the Neotropical fish Brycon henni, Eigenmann 1913 (Characiformes, Bryconidae) Ricardo M. Landı´nez-Garcı´a1, Juan F. Alzate2, and Edna J. Ma´rquez1 Facultad de Ciencias, Universidad Nacional de Colombia, Medellı´n, Colombia and 2Centro Nacional de Secuenciacio´n Geno´mica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellı´n, Colombia
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/06/15 For personal use only.
1
Abstract
Keywords
Brycon henni (Characiformes, Bryconidae) is a trans-Andean omnivorous fish considered as promising species in aquaculture of temperate zones. In this work we report for first time the complete mitochondrial genome of B. henni. This mitogenome spans 16,885 bp and encodes 13 proteins, 22 tRNAs and 2 ribosomal RNAs. Additionally, the synteny is conserved with others species of the order Characiformes.
Freshwater fish, Illumina sequencing, mitogenome, Otophisy
The phylogenetics and taxonomy of the family Bryconidae and its relationships with the order Characiformes have been subject of several controversies (Nakatani et al., 2011; Oliveira et al., 2011). A study about the systematic and historical biogeography of the Bryconidae (Abe et al., 2014) show that the cis- and trans-Andean members of Brycon are not monophyletic and the relationship among cis-Andean species of this clade remain unresolved. Although the mitogenome of Brycon orbignyanus was recently published (Siqueira et al., 2014), a wider sampling of taxas and individuals are required to improve our understanding of the relationships between the families Bryconidae and Characidae. Thus, this work reports the complete mitochondrial genome of B. henni, an trans-Andean omnivorous fish considered as promising in aquaculture of temperate zones (Lenis et al., 2009). In this work, one specimen of B. henni was collected in Cauca river (Colombia) and a sample from skeletal muscle tissue was used for genomic DNA isolation. Sequencing process was performed with Illumina Miseq platform using the whole genome shotgun strategy and 250 bases paired-end reads. Obtained reads were screened for the presence of mitochondrial sequences using a custom database of mitochondrial genomes of related species and the algorithm BLASTN (Bethesda, MD) (Altschul et al., 1997). Filtered reads were then assembled with the NEWBLER package v2.9
History Received 29 October 2014 Accepted 1 November 2014 Published online 25 November 2014
(Branford, CT) (Margulies et al., 2005) and the obtained contig was further annotated using the softwares ARTEMIS v16.0.0 (Cambridge, UK) (Rutherford et al., 2000) and MITOS prediction server (Leipzig, Germany) (Bernt et al., 2013). Annotation conflicts were resolved using MITOFISH web server (Tokyo, Japan) (Iwasaki et al., 2013). The mitogenome of B. henni (GenBank Accession number KP027535) is 16,885 bp in length and the overall base composition is A: 29.65%, C: 28.36%, G: 16.19% and T: 25.77%. This mitogenome contains 13 coding sequences (CDS) related to the respiratory chain, 2 ribosomal RNA genes (rRNA), 22 transfer RNAs and a 1208 bp D-loop region (Figure 1). The CDS sequences correspond to the genes cox1, cox2, atp8, atp6, cox3, nad3, nad4l, nad4, nad5, nad6, cytb, nad1 and nad2. The CDS sequences (except nad6), D-loop and the rRNA genes mt-rnr1 and mt-rnr2 are in the same strand. The 22 tRNA genes distributed in both strands are: trnD(GTC), trnK(TTT), trnG(TCC), trnR(TCG), trnH(GTG), 2 trnS(GCT, TGA), 2 trnL(TAG, TAA), trnE(TTC), trnT(TGT), trnP(TGG), trnF(GAA), trnV(TAC), trnI(GAT), trnQ(TTG), trnM(CAT), trnW(TCA), trnA(TGC), trnN(GTT), trnC(GCA) and trnY(GTA). This mitogenome presents perfect synteny with others members of order Characiformes such as Brycon orbignyanus (Bryconidae), Astyanax mexicanus (Characidae), Curimatopsis evelynae (Curimatidae) and Prochilodus lineatus (Prochilodontidae).
Correspondence: Edna Ma´rquez, Facultad de Ciencias, Universidad Nacional de Colombia, Calle 59A No 63 – 20 Bloque 19 A Laboratorio 310, Medellı´n, Colombia. Tel: (57)(4) 4309072. Fax: (57)(4) 4309116. E-mail: [email protected], [email protected].
2
R. M. Landı´nez-Garcı´a et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Graphical map of the Brycon henni mitochondrial genome. The arrows represent the coding sequences. Small squares represent the tRNA genes. Solid and striped rectangles depict ribosomal RNA genes and D-loop region, respectively. In the center, a histogram represents the GC content.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/06/15 For personal use only.
Brycon henni 16,885 bp
Declaration of interest The author reports no conflict of interest. The authors alone are responsible for content and writing of the paper. This work was funded by the Universidad Nacional de Colombia, Sede Medellı´n and Empresas Pu´blicas de Medellı´n, Grant CT-2013002443 ‘‘Variacio´n genotı´pica y fenotı´pica de poblaciones de especies reo´filas presentes en el a´rea de influencia del proyecto hidroele´ctrico Ituango’’.
References Abe KT, Mariguela TC, Avelino GS, Foresti F, Oliveira C. (2014). Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna. BMC Evol Biol Biol 14:152–67. Altschul SF, Madden TL, Scha¨ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389–402. Bernt M, Donath A, Ju¨hling F, Externbrink F, Florentz C, Fritzsch G, Pu¨tz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial
genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol 30:2531–40. Lenis GA, Restrepo LF, Rivera JC, Monsalve F, Cruz-Casallas PE. (2009). Reproduccio´n inducida y produccio´n de alevinos de sabaleta Brycon henni: Determinacio´n del tiempo de latencia utilizando extracto de hipo´fisis de carpa. Rev Colomb Ciencias Pecu 22:143–55. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, et al. (2005). Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376–80. Nakatani M, Miya M, Mabuchi K, Saitoh K, Nishida M. (2011). Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evol Biol 11:177–202. Oliveira C, Avelino GS, Abe KT, Mariguela TC, Benine RC, Ortı´ G, Vari RP, et al. (2011). Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling. BMC Evol Biol 11: 1–25. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B. (2000). Artemis: Sequence visualization and annotation. Bioinformatics 16:944–5. Siqueira F de F, Carmo AO do, Pimentel J da SM, Kalapothakis E. (2014). Complete mitochondrial genome sequence of Brycon orbignyanus (Characiformes, Bryconidae). Mitochondrial DNA. Available at: http://informahealthcare.com/doi/abs/10.3109/19401736. 2014.971298 (Accessed 28 October 2014).
