Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid. Miguel A. Del Río-Portilla, Carmen E. Vargas-Peralta, Claudia Farfán, Irene de los A. Barriga-Sosa & Francisco J. García-De-León To cite this article: Miguel A. Del Río-Portilla, Carmen E. Vargas-Peralta, Claudia Farfán, Irene de los A. Barriga-Sosa & Francisco J. García-De-León (2014): The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid., Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.947590
Published online: 14 Aug 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Australian National University]
Date: 05 November 2015, At: 15:19
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.947590
MITOGENOME ANNOUNCEMENT
The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid. Miguel A. Del Rı´o-Portilla1, Carmen E. Vargas-Peralta1, Claudia Farfa´n1, Irene de los A. Barriga-Sosa2, and Francisco J. Garcı´a-De-Leo´n3
Downloaded by [Australian National University] at 15:19 05 November 2015
1
Departamento de Acuicultura, Centro de Investigacio´n Cientı´fica y de Educacio´n Superior de Ensenada, B.C., Ensenada, B. C. Me´xico, 2Laboratorio de Gene´tica y Biologı´a Molecular, Planta Experimental de Produccio´n Acuı´cola, Universidad Auto´noma Metropolitana Unidad Iztapalapa, Delegacio´n Iztapalapa, Me´xico, D.F, and 3Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste (CIBNOR), Instituto Polite´cnico Nacional 195, Baja California Sur, Me´xico Abstract
Keywords
The mitogenome of the tenguayaca, Petenia splendida (GenBank accession number KJ914664) has a total length of 16,518 bp, and the arrangement consist of 15 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Gene order was equal to the mitogenomes of other new world cichlids.
Mitochondrial genome, native bay snook, Petenia splendida, tenguayaca History Received 9 July 2014 Accepted 19 July 2014 Published online 13 August 2014
Petenia splendida (Gunter, 1862) is a Neotropical heroine cichlid of the Usumacinta Province. This Province comprises fresh and brackish waters of southeastern Mexico, Guatemala and Belize and harbors over 200 fish species, of which 25% are cichlids (Miller, 1966). Mesoamerican cichlids are mostly secondary freshwater fishes originated in South America and their dispersal and diversification is of great interest. In particular the heroine tribe, a very diverse and specious group, has been the object of a number of molecular phylogenetic studies (Hulsey et al., 2004). Although Petenia splendida is a monotype for the genus, a recent study (Mendez et al., 2011) reported the presence of three morphotypes across its distribution. This species has been included in all recent comprehensive phylogenetic reconstructions based on cytochrome b (Concheriro Pe´rez et al., 2007; Hulsey et al., 2004) nuclear gene sequences or on multilocus analyses (Farias et al., 2000; Hulsey et al., 2011; Lo´pez-Ferna´ndez et al., 2010; Rˇ´ıcˇan et al., 2008). Published specific studies on P. splendida are sparse and mainly related to biological aspects relevant for the development of culture strategies (ArredondoFigueroa et al., 2013; Jime´nez-Martı´nez et al., 2009; Pe´rez-Vega et al., 2006; Vidal-Lo´pez et al., 2009). Here, we present information on the complete mitochondrial genome sequence of Petenia splendida (Genbank accession number KJ914664) from Pantanos de Centla, Frontera, Tabasco (18 240 54.2900 N, 92 340 45.5200 W), Mexico. A tissue sample
Correspondence: Francisco J. Garcı´a-De-Leo´n, Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste (CIBNOR), Instituto Polite´cnico Nacional 195, Colonia Playa Palo de Santa Rita Sur, La Paz 23096, Baja California Sur, Me´xico. E-mail: [email protected]
(2 cm2) from the caudal fin of the fish was dissected and preserved in 95% EtOH. Total DNA was extracted with the WizardÕ Genomic DNA Purification Kit (Promega Coorporation, Woods Hollow Rd. Madison, WI). In construct the libraries, the purified DNA was sheared on a Bioruptor, Illumina TruSeq (San Diego, CA) compatible adapters with custom indexes added using Kapa BioSciences (Boston, MA) library preparation kits, checked for quality, normalized, pooled and run in Illumina MiSeq (paired-end 250 reads) at the Georgia Genomics Facility (University of Georgia). Reads were assembled using CLC-Genomics Workbench 6.5. Gene annotation was carried out using DOGMA (Wyman et al., 2004) and MITOS (Bernt et al., 2013) software, tRNA’s were checked with Mitofish program (Iwasaki et al., 2013). Petenia splendida mitogenome has a total length of 16,518 bp (20 average coverage), the base composition is: A ¼ 28.0%, T ¼ 25.2%, C ¼ 31.3% and G ¼ 15.5%, showing an A + T 53.2% rich feature, similar to new world cichlids mitogenomes (Paraneetroplus synspilus NC_023526, Hypselecara temporalis NC_011168, Astronotus ocellatus NC_009058, Hypselecara temporalis AP009506, Astronotus ocellatus AP009127). The P. splendida mitochondrial genome arrangement consists of 15 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes (trnF-gaa, trnV-tac, trnL-taa, trnI-gat, trnQ-ttg, trnM-cat, trnW-tca, trnA-tgc, trnN-gtt, trnC-gca, trnY-gta, trnS-tga, trnD-gtc, trnK-ttt, trnG-tcc, trnR-tcg, trnH-gtg, trnS-gct, trnL-tag, trnE-ttc, trnT-tgt, trnP-tgg). The mitochondrial structure is similar to other new world cichlids. This mitochondrial genome will provide useful information to clarify its taxonomy, posterior population analyses of this species and phylogenetic relation with other new world cichlids (Figure 1).
2
M. A. Del Rı´o-Portilla et al.
Mitochondrial DNA, Early Online: 1–2
Downloaded by [Australian National University] at 15:19 05 November 2015
Figure 1. Phylogenetic three of the new world cichlids mitogenomes found in the GenBank (April 2014; Accession number on the right), Petenia splendida (from this study) and tilapia, Oreochromis aureus, O. niloticus and O. mossambicus, as references.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Support was provided by CICESE and CIBNOR through the Subsistema Nacional de Recursos Gene´ticos Acua´ticos, SUBNARGENA, of the Secretarı´a de Ganaderı´a, Agricultura, Desarrollo Rural, Pesca y Alimentacio´n, SAGARPA and to PDCBS Ref. 14707.03 granted to IDLABS. Authors thank to Dra. M Hilda Pe´rez Vega for donating the specimen P. splendida utilized in the present study and to R. Delgado Vega for technical assistance.
References Arredondo-Figueroa JL, Nu´n˜ez-Garcı´a L, Pe´rez-Vega M, Ponce-Palafox JT, Barriga-Sosa I. (2013). Culture of founders and breeding of the Bay Snook Petenia splendida (Pisces: Cichlidae) in a recirculation aquaculture system. EIJST 2:123–32. Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz, et al. 2013. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Concheiro Pe´rez GA, Rˇ´ıcˇan O, Orti G, Berminingham E, Doadrio I, Zardoya R. (2007). Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol Phylogenet Evol 41:91–10. Farias IP, Orti G, Meyer A. (2000). Total evidence: Molecules, morphology, and the phylogenetics of cichlid fishes. J Exp Zool 288:76–92. Gu¨nther A. (1862). A catalogue of the fishes in the British Museum. Nat. Hist. IV:264–316. Hulsey CD, Garcı´a de Leo´n FJ, Sa´nchez Johnson Y, Hendrickson DA, Near TJ. (2004). Temporal diversification of Mesoamarican cichlid fishes across a major biogeographic boundary. Mol Phylogenet Evol 31:754–64. Hulsey CD, Keck BP, Hollingsworth Jr PR. (2011). Species tree estimation and the historical biogeography of heroine cichlids. Mol Phylogenet Evol 58:124–31.
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. Jime´nez-Martı´nez LD, Alvarez-Gonza´lez CA, Contreras-Sa´nchez WM, Ma´rquez Couturier G, Arias-Rodrı´guez L, Almeida-Madrigal J. (2009). Evaluation of larval growth and survival in Mexican Mojarra Cichlasoma urophthalmus, and Bay Snook, Petenia splendida, under different initial stocking densities. J World Aquacult Soc 40: 753–60. Lo´pez-Ferna´ndez H, Winemiller KO, Honeycutt RL. (2010). Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae). Mol Phylogenet Evol 5:1070–86. Me´ndez A, ME Garcı´a, L Lozano. (2011). Sistema´tica del pez Petenia splendida (Perciformes: Cichlidae) en el lago Pete´n Itza´, Guatemala. Rev Biol Trop 59:1205–16. Miller RR. (1966). Geographical distribution of Central American freshwater fishes. Copeia 4:733–802. Pe´rez-Vega HM, Uribe-Aranzabal CM, Garcı´a-Lorenzana M, RomeroRamı´rez C, Arredondo-Figueroa JL. (2006). Description of the ovarian follicle growth of the Neotropical cichlids Petenia splendida and Parachromis managuensis (Perciformes: Cichlidae). J Appl Ichthyol 22:515–20. Rˇ´ıcˇan O, Zardoya R, Doadrio I. (2008). Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology. Mol Phylogenet Evol 49:941–57. Vidal-Lo´pez JM, Alvarez-Gonza´lez CA, Contreras-Sa´nchez WM, Herna´ndez-Vidal U. (2009). Mazculinization of the native cichlid Tenhuayaca, Petenia splendida (Gu¨nther, 1862), using Artemia nauplii as vehicle of the steroid 17-a methyltestosterone. Hidrobiolo´gica 19: 211–16. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid. Miguel A. Del Río-Portilla, Carmen E. Vargas-Peralta, Claudia Farfán, Irene de los A. Barriga-Sosa & Francisco J. García-De-León To cite this article: Miguel A. Del Río-Portilla, Carmen E. Vargas-Peralta, Claudia Farfán, Irene de los A. Barriga-Sosa & Francisco J. García-De-León (2014): The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid., Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.947590
Published online: 14 Aug 2014.
Submit your article to this journal
Article views: 15
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Australian National University]
Date: 05 November 2015, At: 15:19
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.947590
MITOGENOME ANNOUNCEMENT
The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid. Miguel A. Del Rı´o-Portilla1, Carmen E. Vargas-Peralta1, Claudia Farfa´n1, Irene de los A. Barriga-Sosa2, and Francisco J. Garcı´a-De-Leo´n3
Downloaded by [Australian National University] at 15:19 05 November 2015
1
Departamento de Acuicultura, Centro de Investigacio´n Cientı´fica y de Educacio´n Superior de Ensenada, B.C., Ensenada, B. C. Me´xico, 2Laboratorio de Gene´tica y Biologı´a Molecular, Planta Experimental de Produccio´n Acuı´cola, Universidad Auto´noma Metropolitana Unidad Iztapalapa, Delegacio´n Iztapalapa, Me´xico, D.F, and 3Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste (CIBNOR), Instituto Polite´cnico Nacional 195, Baja California Sur, Me´xico Abstract
Keywords
The mitogenome of the tenguayaca, Petenia splendida (GenBank accession number KJ914664) has a total length of 16,518 bp, and the arrangement consist of 15 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Gene order was equal to the mitogenomes of other new world cichlids.
Mitochondrial genome, native bay snook, Petenia splendida, tenguayaca History Received 9 July 2014 Accepted 19 July 2014 Published online 13 August 2014
Petenia splendida (Gunter, 1862) is a Neotropical heroine cichlid of the Usumacinta Province. This Province comprises fresh and brackish waters of southeastern Mexico, Guatemala and Belize and harbors over 200 fish species, of which 25% are cichlids (Miller, 1966). Mesoamerican cichlids are mostly secondary freshwater fishes originated in South America and their dispersal and diversification is of great interest. In particular the heroine tribe, a very diverse and specious group, has been the object of a number of molecular phylogenetic studies (Hulsey et al., 2004). Although Petenia splendida is a monotype for the genus, a recent study (Mendez et al., 2011) reported the presence of three morphotypes across its distribution. This species has been included in all recent comprehensive phylogenetic reconstructions based on cytochrome b (Concheriro Pe´rez et al., 2007; Hulsey et al., 2004) nuclear gene sequences or on multilocus analyses (Farias et al., 2000; Hulsey et al., 2011; Lo´pez-Ferna´ndez et al., 2010; Rˇ´ıcˇan et al., 2008). Published specific studies on P. splendida are sparse and mainly related to biological aspects relevant for the development of culture strategies (ArredondoFigueroa et al., 2013; Jime´nez-Martı´nez et al., 2009; Pe´rez-Vega et al., 2006; Vidal-Lo´pez et al., 2009). Here, we present information on the complete mitochondrial genome sequence of Petenia splendida (Genbank accession number KJ914664) from Pantanos de Centla, Frontera, Tabasco (18 240 54.2900 N, 92 340 45.5200 W), Mexico. A tissue sample
Correspondence: Francisco J. Garcı´a-De-Leo´n, Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste (CIBNOR), Instituto Polite´cnico Nacional 195, Colonia Playa Palo de Santa Rita Sur, La Paz 23096, Baja California Sur, Me´xico. E-mail: [email protected]
(2 cm2) from the caudal fin of the fish was dissected and preserved in 95% EtOH. Total DNA was extracted with the WizardÕ Genomic DNA Purification Kit (Promega Coorporation, Woods Hollow Rd. Madison, WI). In construct the libraries, the purified DNA was sheared on a Bioruptor, Illumina TruSeq (San Diego, CA) compatible adapters with custom indexes added using Kapa BioSciences (Boston, MA) library preparation kits, checked for quality, normalized, pooled and run in Illumina MiSeq (paired-end 250 reads) at the Georgia Genomics Facility (University of Georgia). Reads were assembled using CLC-Genomics Workbench 6.5. Gene annotation was carried out using DOGMA (Wyman et al., 2004) and MITOS (Bernt et al., 2013) software, tRNA’s were checked with Mitofish program (Iwasaki et al., 2013). Petenia splendida mitogenome has a total length of 16,518 bp (20 average coverage), the base composition is: A ¼ 28.0%, T ¼ 25.2%, C ¼ 31.3% and G ¼ 15.5%, showing an A + T 53.2% rich feature, similar to new world cichlids mitogenomes (Paraneetroplus synspilus NC_023526, Hypselecara temporalis NC_011168, Astronotus ocellatus NC_009058, Hypselecara temporalis AP009506, Astronotus ocellatus AP009127). The P. splendida mitochondrial genome arrangement consists of 15 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes (trnF-gaa, trnV-tac, trnL-taa, trnI-gat, trnQ-ttg, trnM-cat, trnW-tca, trnA-tgc, trnN-gtt, trnC-gca, trnY-gta, trnS-tga, trnD-gtc, trnK-ttt, trnG-tcc, trnR-tcg, trnH-gtg, trnS-gct, trnL-tag, trnE-ttc, trnT-tgt, trnP-tgg). The mitochondrial structure is similar to other new world cichlids. This mitochondrial genome will provide useful information to clarify its taxonomy, posterior population analyses of this species and phylogenetic relation with other new world cichlids (Figure 1).
2
M. A. Del Rı´o-Portilla et al.
Mitochondrial DNA, Early Online: 1–2
Downloaded by [Australian National University] at 15:19 05 November 2015
Figure 1. Phylogenetic three of the new world cichlids mitogenomes found in the GenBank (April 2014; Accession number on the right), Petenia splendida (from this study) and tilapia, Oreochromis aureus, O. niloticus and O. mossambicus, as references.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Support was provided by CICESE and CIBNOR through the Subsistema Nacional de Recursos Gene´ticos Acua´ticos, SUBNARGENA, of the Secretarı´a de Ganaderı´a, Agricultura, Desarrollo Rural, Pesca y Alimentacio´n, SAGARPA and to PDCBS Ref. 14707.03 granted to IDLABS. Authors thank to Dra. M Hilda Pe´rez Vega for donating the specimen P. splendida utilized in the present study and to R. Delgado Vega for technical assistance.
References Arredondo-Figueroa JL, Nu´n˜ez-Garcı´a L, Pe´rez-Vega M, Ponce-Palafox JT, Barriga-Sosa I. (2013). Culture of founders and breeding of the Bay Snook Petenia splendida (Pisces: Cichlidae) in a recirculation aquaculture system. EIJST 2:123–32. Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz, et al. 2013. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Concheiro Pe´rez GA, Rˇ´ıcˇan O, Orti G, Berminingham E, Doadrio I, Zardoya R. (2007). Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol Phylogenet Evol 41:91–10. Farias IP, Orti G, Meyer A. (2000). Total evidence: Molecules, morphology, and the phylogenetics of cichlid fishes. J Exp Zool 288:76–92. Gu¨nther A. (1862). A catalogue of the fishes in the British Museum. Nat. Hist. IV:264–316. Hulsey CD, Garcı´a de Leo´n FJ, Sa´nchez Johnson Y, Hendrickson DA, Near TJ. (2004). Temporal diversification of Mesoamarican cichlid fishes across a major biogeographic boundary. Mol Phylogenet Evol 31:754–64. Hulsey CD, Keck BP, Hollingsworth Jr PR. (2011). Species tree estimation and the historical biogeography of heroine cichlids. Mol Phylogenet Evol 58:124–31.
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. Jime´nez-Martı´nez LD, Alvarez-Gonza´lez CA, Contreras-Sa´nchez WM, Ma´rquez Couturier G, Arias-Rodrı´guez L, Almeida-Madrigal J. (2009). Evaluation of larval growth and survival in Mexican Mojarra Cichlasoma urophthalmus, and Bay Snook, Petenia splendida, under different initial stocking densities. J World Aquacult Soc 40: 753–60. Lo´pez-Ferna´ndez H, Winemiller KO, Honeycutt RL. (2010). Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae). Mol Phylogenet Evol 5:1070–86. Me´ndez A, ME Garcı´a, L Lozano. (2011). Sistema´tica del pez Petenia splendida (Perciformes: Cichlidae) en el lago Pete´n Itza´, Guatemala. Rev Biol Trop 59:1205–16. Miller RR. (1966). Geographical distribution of Central American freshwater fishes. Copeia 4:733–802. Pe´rez-Vega HM, Uribe-Aranzabal CM, Garcı´a-Lorenzana M, RomeroRamı´rez C, Arredondo-Figueroa JL. (2006). Description of the ovarian follicle growth of the Neotropical cichlids Petenia splendida and Parachromis managuensis (Perciformes: Cichlidae). J Appl Ichthyol 22:515–20. Rˇ´ıcˇan O, Zardoya R, Doadrio I. (2008). Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology. Mol Phylogenet Evol 49:941–57. Vidal-Lo´pez JM, Alvarez-Gonza´lez CA, Contreras-Sa´nchez WM, Herna´ndez-Vidal U. (2009). Mazculinization of the native cichlid Tenhuayaca, Petenia splendida (Gu¨nther, 1862), using Artemia nauplii as vehicle of the steroid 17-a methyltestosterone. Hidrobiolo´gica 19: 211–16. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
