http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.953075
MITOGENOME ANNOUNCEMENT
Lionfish, Pterois volitans Linnaeus 1758, the complete mitochondrial DNA of an invasive species Miguel A. Del Rı´o-Portilla1, Carmen E. Vargas-Peralta1, Salima Machkour-M’Rabet2, Yann He´naut3, and Francisco J. Garcı´a-De-Leo´n4
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/16/15 For personal use only.
1
Departamento de Acuicultura, Centro de Investigacio´n Cientı´fica y de Educacio´n Superior de Ensenada, BC, Me´xico, 2Laboratorio de Ecologı´a Molecular y Conservacio´n, GAIA-BIO, El Colegio de la Frontera Sur (ECOSUR), Chetumal, Quintana Roo, Mexico, 3Laboratorio de Conducta Animal y Etologı´a Aplicada, GAIA-BIO, El Colegio de la Frontera Sur (ECOSUR), Chetumal, Quintana Roo, Mexico, and 4Laboratorio 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, Baja California Sur, Me´xico Abstract
Keywords
The lionfish, Pterois volitans, native from the Indo-Pacific, has been found in Atlantic and Caribbean waters and is considered as an invasive species. Here we sequence its mitogenome (Genbank accession number KJ739816), which has a total length of 16,500 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA similar to other Pteroinae subfamily (family Scorpaenidae). This mitogenome will be useful for phylogenetic and population genetic studies of this invasive species.
Invasive species, mitochondrial genome, Pterois volitans
The lionfish, Pterois volitans Linnaeus 1758, is a very popular species among aquarists and is native from the Indo-Pacific region. However, nowadays it has been found in the Atlantic (Whitfield et al., 2002) and in Mexican Caribbean, (BritoBermudez et al., 2014). In order to increase the genetic knowledge of this species, we sequenced its complete mitochondrial genome from a specimen found in Mexico. A lionfish was collected in Mahahual (18 710 N-87 710 W), Quintana Roo, Mexico by snorkeling (55 m of depth) with a hand net, and transported into the laboratory of ‘‘el Colegio de la Frontera Sur’’. Pectoral fin tissue samples were preserved in 96% ethanol. Total DNA was extracted with EZNA DNA purification kit (Omega Bio-Tek, Norcross, GA). DNA libraries were constructed by shearing the DNA on Bioruptor Illumina TruSeq (Illumina, San Diego, CA) compatible adapters with custom indexes added using Kapa BioSciences library (KapaBiosystems, Woburn, MA) preparation kits, checked for quality, normalized, pooled and run an Illumina MiSeq (paired-end 250 reads, Illumina, San Diego, CA) at the Georgia Genomics Facility (University of Georgia). Reads were assembled using CLC-Genomics Workbench V. 6.5 (CLC-Bio, www.clcbio.com). Gene annotation was carried out using DOGMA (Wyman et al., 2004) and MITOS (Bernt et al., 2013) software. tRNA gene inconsistencies were 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]
History Received 9 July 2014 Revised 30 July 2014 Accepted 6 August 2014 Published online 29 August 2014
resolved using the tRNAscan-SE (Lowe & Eddy, 1997), RFAm (Griffiths-Jones et al., 2003) and Mitofish (Iwasaki et al., 2013) programs. Pterois volitans mitogenome (GeneBank accession number KJ739816) has a total length of 16,500 bp (35.44 X average coverage) with a genome base composition: A 27.6%, T 25.6%, C 28.9% and G 18.0%, with an A + T (53.1%) rich feature, similar to other Scorpaeniformes mitogenomes. The mitochondrial genome arrangement consists of 13 proteincoding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNAs, and its structure and gene order (Table 1) are similar to other species of the Scorpaeniformes. A tRNA-Ser (AGY) was found with Mitos at 11,820–11,887 nucleotides and Mitofish annotator, but RFam and the TRNAscan-SE did not corroborate the tRNA. This gene (a tRNA-Ser-AGY) is found in Sebastes koreanus (GeneBank accession number KF561237) and Sebates schlegeli (GeneBank accession number AY491978) at positions 11,806–11,873 and 11,834–11,901, respectively. Therefore we annotated this tRNA in P. volitans. Further comparison with other P. volitans sequences in the GenBank (until 7 April 2014) showed that the sequence here described (KJ739816) was identical to the control region (FJ516410) from an specimen found in the North Atlantic/ Caribbean Sea (Freshwater et al., 2009), while it had three nucleotide differences with AJ628936 from Taiwan (Kochzius & Blohm, 2005). Also KJ739816 was the same, at the 16S gene, to AJ429409 (Kochzius et al., 2003) while at Cytochrome B gene, KJ739816 was similar to AJ429432 (Kochzius et al., 2003) except for four nucleotides, but did not produced an amino acid change at
2
M. A. D. Rı´o-Portilla et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Mitogenome gene order of the lionfish, Pterois volitans.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/16/15 For personal use only.
Start 1 69 1019 1092 2796 2870 3849 3918 3988 4057 5103 5175 5245 5354 5421 5492 7044 7119 7197 7888 7964 8122 8805 9590 9662 10,011 10,080 10,370 11,751 11,820 11,892 11,965 13,800 14,322 14,397 15,538 15,609
Acknowledgements
End
Length (bp)
Gene Name
Strand
68 1014 1091 2795 2869 3844 3918 3988 4056 5103 5173 5243 5317 5420 5490 7042 7114 7191 7887 7962 8135 8805 9590 9661 10,012 10,079 10,376 11,750 11,819 11,887 11,964 13,801 14,321 14,390 15,537 15,609 15,678
67 945 72 1703 73 974 69 70 68 1046 70 68 72 66 69 1550 70 72 690 74 171 683 785 71 350 68 296 1380 68 68 72 1836 521 68 1140 71 69
tRNA-Phe-gaa 12sRNA tRNA-Val-uac 16sRNA tRNA-Leu-uaa NAD1 tRNA-Ile-gau tRNA-Gln-uug tRNA-Met-cau NAD2 tRNA-Trp-uca tRNA-Ala-ugc tRNA-Asn-guu tRNA-Cys-gca tRNA-Tyr-gua COX1 tRNA-Ser-uga tRNA-Asp-guc COX2 tRNA-Lys-uuu ATP8 ATP6 COX3 tRNA-Gly-ucc NAD3 tRNA-Arg-ucg NAD4L NAD4 tRNA-His-gug tRNA-Ser AGY tRNA-Leu-uag NAD5 NAD6 tRNA-Glu-uuc CYTB tRNA-Thr-ugu tRNA-Pro-ugg
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
protein level. The information of the Pterois volitans mitogenome given here will be useful in phylogenetic and population genetics analysis studies among others, since this is the first mitogenome described for this genus and the Pteroinae subfamily (family Scorpaenidae).
The authors thank Maria del Carmen Garcia Rivas, director of Banco Chinchorro Biosphere Reserve and National Reef Park of Xcalak, CONANP-SEMARNAT, for technical support.
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.
References Bernt M, Donath A, Ju¨hling, F, Externbrink F, Florentz C, Fritzsch G, Stadler PF, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Brito-Bermu´dez A, Gonza´lez-Baca CA, Go´mez Lozano FR. (2014). Invasio´n, reaccio´n y accio´n. La cro´nica de la invasio´n del pez leo´n (Pterois spp.) En el caribe mexicano. In: Mendoza-Alfaro RE, KoleffOsorio P. (Co-ord.) Especies Acua´ticas Invasoras en Me´xico. p 465–8. Freshwater DW, Hines A, Parham S, Wilbur A, Sabaoun M, Woodhead J, Paris CB, et al. (2009). Mitochondrial control region sequence analyses indicate dispersal from the US East Coast as the source of the invasive Indo-Pacific lionfish Pterois volitans in the Bahamas. Marine Biol 156: 1213–21. Griffiths-Jones S, Bateman A, Marshall M, Khanna A. Eddy SR. (2003). Rfam: An RNA family database. Nucleic Acids Res 31:439–41. 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. Kochzius M, Blohm D. (2005). Genetic population structure of the lionfish Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red Sea. Gene 347:295–301. Kochzius M, So¨ller R, Khalaf MA, Blohm D. (2003). Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences. Mol Phylogenet Evol 28:396–403. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Whitfield PE, Gardner T, Vives SP, Gilligan MR Jr, Courtenay WR, Ray GC, Hare JA. (2002). Biological invasion of the Indo-Pacific lionfish Pterois volitans along the Atlantic coast of North America. Mar Ecol Prog Ser 235:289–97. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics (Oxford, England) 20:3252–5.
MITOGENOME ANNOUNCEMENT
Lionfish, Pterois volitans Linnaeus 1758, the complete mitochondrial DNA of an invasive species Miguel A. Del Rı´o-Portilla1, Carmen E. Vargas-Peralta1, Salima Machkour-M’Rabet2, Yann He´naut3, and Francisco J. Garcı´a-De-Leo´n4
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/16/15 For personal use only.
1
Departamento de Acuicultura, Centro de Investigacio´n Cientı´fica y de Educacio´n Superior de Ensenada, BC, Me´xico, 2Laboratorio de Ecologı´a Molecular y Conservacio´n, GAIA-BIO, El Colegio de la Frontera Sur (ECOSUR), Chetumal, Quintana Roo, Mexico, 3Laboratorio de Conducta Animal y Etologı´a Aplicada, GAIA-BIO, El Colegio de la Frontera Sur (ECOSUR), Chetumal, Quintana Roo, Mexico, and 4Laboratorio 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, Baja California Sur, Me´xico Abstract
Keywords
The lionfish, Pterois volitans, native from the Indo-Pacific, has been found in Atlantic and Caribbean waters and is considered as an invasive species. Here we sequence its mitogenome (Genbank accession number KJ739816), which has a total length of 16,500 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA similar to other Pteroinae subfamily (family Scorpaenidae). This mitogenome will be useful for phylogenetic and population genetic studies of this invasive species.
Invasive species, mitochondrial genome, Pterois volitans
The lionfish, Pterois volitans Linnaeus 1758, is a very popular species among aquarists and is native from the Indo-Pacific region. However, nowadays it has been found in the Atlantic (Whitfield et al., 2002) and in Mexican Caribbean, (BritoBermudez et al., 2014). In order to increase the genetic knowledge of this species, we sequenced its complete mitochondrial genome from a specimen found in Mexico. A lionfish was collected in Mahahual (18 710 N-87 710 W), Quintana Roo, Mexico by snorkeling (55 m of depth) with a hand net, and transported into the laboratory of ‘‘el Colegio de la Frontera Sur’’. Pectoral fin tissue samples were preserved in 96% ethanol. Total DNA was extracted with EZNA DNA purification kit (Omega Bio-Tek, Norcross, GA). DNA libraries were constructed by shearing the DNA on Bioruptor Illumina TruSeq (Illumina, San Diego, CA) compatible adapters with custom indexes added using Kapa BioSciences library (KapaBiosystems, Woburn, MA) preparation kits, checked for quality, normalized, pooled and run an Illumina MiSeq (paired-end 250 reads, Illumina, San Diego, CA) at the Georgia Genomics Facility (University of Georgia). Reads were assembled using CLC-Genomics Workbench V. 6.5 (CLC-Bio, www.clcbio.com). Gene annotation was carried out using DOGMA (Wyman et al., 2004) and MITOS (Bernt et al., 2013) software. tRNA gene inconsistencies were 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]
History Received 9 July 2014 Revised 30 July 2014 Accepted 6 August 2014 Published online 29 August 2014
resolved using the tRNAscan-SE (Lowe & Eddy, 1997), RFAm (Griffiths-Jones et al., 2003) and Mitofish (Iwasaki et al., 2013) programs. Pterois volitans mitogenome (GeneBank accession number KJ739816) has a total length of 16,500 bp (35.44 X average coverage) with a genome base composition: A 27.6%, T 25.6%, C 28.9% and G 18.0%, with an A + T (53.1%) rich feature, similar to other Scorpaeniformes mitogenomes. The mitochondrial genome arrangement consists of 13 proteincoding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNAs, and its structure and gene order (Table 1) are similar to other species of the Scorpaeniformes. A tRNA-Ser (AGY) was found with Mitos at 11,820–11,887 nucleotides and Mitofish annotator, but RFam and the TRNAscan-SE did not corroborate the tRNA. This gene (a tRNA-Ser-AGY) is found in Sebastes koreanus (GeneBank accession number KF561237) and Sebates schlegeli (GeneBank accession number AY491978) at positions 11,806–11,873 and 11,834–11,901, respectively. Therefore we annotated this tRNA in P. volitans. Further comparison with other P. volitans sequences in the GenBank (until 7 April 2014) showed that the sequence here described (KJ739816) was identical to the control region (FJ516410) from an specimen found in the North Atlantic/ Caribbean Sea (Freshwater et al., 2009), while it had three nucleotide differences with AJ628936 from Taiwan (Kochzius & Blohm, 2005). Also KJ739816 was the same, at the 16S gene, to AJ429409 (Kochzius et al., 2003) while at Cytochrome B gene, KJ739816 was similar to AJ429432 (Kochzius et al., 2003) except for four nucleotides, but did not produced an amino acid change at
2
M. A. D. Rı´o-Portilla et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Mitogenome gene order of the lionfish, Pterois volitans.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Otago on 07/16/15 For personal use only.
Start 1 69 1019 1092 2796 2870 3849 3918 3988 4057 5103 5175 5245 5354 5421 5492 7044 7119 7197 7888 7964 8122 8805 9590 9662 10,011 10,080 10,370 11,751 11,820 11,892 11,965 13,800 14,322 14,397 15,538 15,609
Acknowledgements
End
Length (bp)
Gene Name
Strand
68 1014 1091 2795 2869 3844 3918 3988 4056 5103 5173 5243 5317 5420 5490 7042 7114 7191 7887 7962 8135 8805 9590 9661 10,012 10,079 10,376 11,750 11,819 11,887 11,964 13,801 14,321 14,390 15,537 15,609 15,678
67 945 72 1703 73 974 69 70 68 1046 70 68 72 66 69 1550 70 72 690 74 171 683 785 71 350 68 296 1380 68 68 72 1836 521 68 1140 71 69
tRNA-Phe-gaa 12sRNA tRNA-Val-uac 16sRNA tRNA-Leu-uaa NAD1 tRNA-Ile-gau tRNA-Gln-uug tRNA-Met-cau NAD2 tRNA-Trp-uca tRNA-Ala-ugc tRNA-Asn-guu tRNA-Cys-gca tRNA-Tyr-gua COX1 tRNA-Ser-uga tRNA-Asp-guc COX2 tRNA-Lys-uuu ATP8 ATP6 COX3 tRNA-Gly-ucc NAD3 tRNA-Arg-ucg NAD4L NAD4 tRNA-His-gug tRNA-Ser AGY tRNA-Leu-uag NAD5 NAD6 tRNA-Glu-uuc CYTB tRNA-Thr-ugu tRNA-Pro-ugg
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
protein level. The information of the Pterois volitans mitogenome given here will be useful in phylogenetic and population genetics analysis studies among others, since this is the first mitogenome described for this genus and the Pteroinae subfamily (family Scorpaenidae).
The authors thank Maria del Carmen Garcia Rivas, director of Banco Chinchorro Biosphere Reserve and National Reef Park of Xcalak, CONANP-SEMARNAT, for technical support.
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.
References Bernt M, Donath A, Ju¨hling, F, Externbrink F, Florentz C, Fritzsch G, Stadler PF, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Brito-Bermu´dez A, Gonza´lez-Baca CA, Go´mez Lozano FR. (2014). Invasio´n, reaccio´n y accio´n. La cro´nica de la invasio´n del pez leo´n (Pterois spp.) En el caribe mexicano. In: Mendoza-Alfaro RE, KoleffOsorio P. (Co-ord.) Especies Acua´ticas Invasoras en Me´xico. p 465–8. Freshwater DW, Hines A, Parham S, Wilbur A, Sabaoun M, Woodhead J, Paris CB, et al. (2009). Mitochondrial control region sequence analyses indicate dispersal from the US East Coast as the source of the invasive Indo-Pacific lionfish Pterois volitans in the Bahamas. Marine Biol 156: 1213–21. Griffiths-Jones S, Bateman A, Marshall M, Khanna A. Eddy SR. (2003). Rfam: An RNA family database. Nucleic Acids Res 31:439–41. 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. Kochzius M, Blohm D. (2005). Genetic population structure of the lionfish Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red Sea. Gene 347:295–301. Kochzius M, So¨ller R, Khalaf MA, Blohm D. (2003). Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences. Mol Phylogenet Evol 28:396–403. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Whitfield PE, Gardner T, Vives SP, Gilligan MR Jr, Courtenay WR, Ray GC, Hare JA. (2002). Biological invasion of the Indo-Pacific lionfish Pterois volitans along the Atlantic coast of North America. Mar Ecol Prog Ser 235:289–97. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics (Oxford, England) 20:3252–5.
