http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1030628
MITOGENOME ANNOUNCEMENT
Genetic variability between complete mitochondrion genomes of the sablefish, Anoplopoma fimbria (Pallas, 1814) Carolina Galva´n-Tirado1, Miguel Angel del Rı´o-Portilla2, Rigoberto Delgado-Vega2, and Francisco J. Garcı´a-De Leo´n1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/15/15 For personal use only.
Laboratorio 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 and 2Departamento de Acuicultura, Centro de Investigacio´n Cientı´fica y de Educacio´n Superior de Ensenada, BC, Me´xico Abstract
Keywords
The complete mitochondrial genome of the sablefish, Anoplopoma fimbria (Genbank accession KP777542) is 16,507 bp in size and contains the typical 37 genes (13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA) found in teleosts mitogenomes. The genome varies in 118 positions with respect to another mitogenome sablefish specimen.
Anoplopoma fimbria, mitochondrial DNA, Sablefish History Received 16 February 2015 Revised 10 March 2015 Accepted 14 March 2015 Published online 11 June 2015
The sablefish, Anoplopoma fimbria (Pallas, 1814), is a deep-water marine species endemic to the North Pacific Ocean. This species is a fishery resource with high commercial value primarily in EEUU and Canada, and it is a promising aquaculture species. However, in Mexico, the sablefish is an unexploited and poorly studied resource (Tripp-Valdez et al., 2012). The complete mitochondrial DNA from a specimen of A. fimbria collected in Ensenada, Mexico (32 30 29.7800 N– 117 480 9.7200 W), was sequenced. The tissue sample coding as bac(A) is placed in the laboratory collection of the Laboratorio de Gene´tica para la Conservacio´n (CIBNOR, Mexico). Genomic 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 Inc., San Diego, CA) compatible adapters with custom indexes added using library preparation kits (KapaBiosystems, Woburn, MA), checked for quality, normalized, pooled, and run an Illumina MiSeq (paired-end 250 reads, Illumina Inc., San Diego, CA) at the Georgia Genomics Facility (University of Georgia). The read quality, trimming, and de novo assembly were performed using CLC Genomics Workbench 6.5 (CLC Bio, Boston, MA). The largest contig was used to annotate gene identity and position with different programs: DOGMA (Wyman et al., 2004), MITOS (Bernt et al., 2013), and MITOFISH (Iwasaki et al., 2013). The contig was compared with other 15 Actinopterygii full mitogenome sequences available in GenBank to resolve gene Correspondence: Francisco J. Garcı´a-De Leo´n, Laboratorio de Gene´tica para la Conservacio´n Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S. 23096, Me´xico. E-mail: [email protected]
inconsistencies, to determine the origin of replication and to infer phylogenetic relationships. The alignment and the Neighbor Joining phylogenetic tree were performed in Mega 6 (MEGA Inc., Englewood, NJ) (Tamura, et al. 2013). The length of the mitogenome of A. fimbria (Genbank accession KP777542) is 16,507 bp with a base composition of A 26.1%, C 29.6%, G 18.3%, and T 26%. The genome contains 11 genes encoding subunits of respiratory chain complexes (COX I– III, CYTB, ND subunits 1–6) and two genes encoding ATP synthase subunits. Genes are carried principally by heavy DNA strand, with the gene order ND1–ND2–COX1–COX2–ATP8– ATP6–COX3–ND3–ND4L–ND4–ND5–CYTB, and ND6 in the light strand. It also encodes 22 tRNAs and the 12S and 16S rRNAs subunits. The mitochondrial arrangement was similar to the sablefish’s mitogenome from Genbank (accession number JX070112.1). The genome varies in 118 positions present in 12S, tRNA-Val, 16S, ND 1-6, tRNA-Asn, COX1, ATP8, ATP6, COX3, and CYTB genes. The ND4 gene showed the highest number of differences, but only the ND2 presented an amino acid translation change from Valine to Isoleucine in the 4653–4655 position. The genetic distance between both mitogenomes of the sablefish was 0.7%. These differences support the hypothesis of at least two sablefish populations in the northeast Pacific (Tripp-Valdez et al., 2012). Although the phylogenetic tree showed that most nodes supported by high-bootstrap percentages, the phylogenetic position of the sablefish was unclear since it was placed as an ancestral node between two clear clades formed by Scorpaeniformes and Perciformes (Figure 1). Similar results were reported by Rondeau et al. (2013) so more information is needed in order to correctly classify the sablefish.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/15/15 For personal use only.
2
C. Galva´n-Tirado et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic relationships among Actinopterygii sequences with the neighbor-joining method. Numbers at the nodes are bootstrap percentages. GenBank accession numbers: Anarhichas lupus (EF427916.1), Anarhichas minor (EF427917), Cottus czerskii (KJ956027.1), Cottus poecilopus (EU332750), Enophrys diceraus (KF039715.1), Gymnocephalus cernua (KM978956.1), Hexagrammos_agrammus (AB763992.1), Lycodes toyamensis (AP004448.1), Mesocottus haitej (KF170219.1), Pholis crassispina (AP004449), Pleurogrammus azonus (AB744047), Pleurogrammus_monopterygius (AB753026.1), Scaliscus amiscus (NC_004403), Sebastes schlegelii (AY491978), and Trachidermus fasciatus (JX017305.1).
Declaration of interest The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Funds were received from CIBNOR and CICESE through the SUBNARGENA and SAGARPA of Mexico and CONACYT Grant 2005-12058 to F. J. G. D. L.
References 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.
Rondeau, EB, Messmer AM, Sanderson DS, Jantzen SG, von Schalburg KR, Minkley DR, Leong JS, et al. (2013) Genomics of sablefish (Anoplopoma fimbria): Expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene. BMC Genom 14:452. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9. Tripp-Valdez MA, Garcı´a-De Leo´n FJ, Espinosa-Pe´rez H, Ruiz-Campos G. (2012) Population structure of sablefish Anoplopoma fimbria using genetic variability and geometric morphometric analysis. J Appl Ichthyol 28:516–23. Wyman SK, Jansen RK, Boore JL. (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
MITOGENOME ANNOUNCEMENT
Genetic variability between complete mitochondrion genomes of the sablefish, Anoplopoma fimbria (Pallas, 1814) Carolina Galva´n-Tirado1, Miguel Angel del Rı´o-Portilla2, Rigoberto Delgado-Vega2, and Francisco J. Garcı´a-De Leo´n1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/15/15 For personal use only.
Laboratorio 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 and 2Departamento de Acuicultura, Centro de Investigacio´n Cientı´fica y de Educacio´n Superior de Ensenada, BC, Me´xico Abstract
Keywords
The complete mitochondrial genome of the sablefish, Anoplopoma fimbria (Genbank accession KP777542) is 16,507 bp in size and contains the typical 37 genes (13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA) found in teleosts mitogenomes. The genome varies in 118 positions with respect to another mitogenome sablefish specimen.
Anoplopoma fimbria, mitochondrial DNA, Sablefish History Received 16 February 2015 Revised 10 March 2015 Accepted 14 March 2015 Published online 11 June 2015
The sablefish, Anoplopoma fimbria (Pallas, 1814), is a deep-water marine species endemic to the North Pacific Ocean. This species is a fishery resource with high commercial value primarily in EEUU and Canada, and it is a promising aquaculture species. However, in Mexico, the sablefish is an unexploited and poorly studied resource (Tripp-Valdez et al., 2012). The complete mitochondrial DNA from a specimen of A. fimbria collected in Ensenada, Mexico (32 30 29.7800 N– 117 480 9.7200 W), was sequenced. The tissue sample coding as bac(A) is placed in the laboratory collection of the Laboratorio de Gene´tica para la Conservacio´n (CIBNOR, Mexico). Genomic 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 Inc., San Diego, CA) compatible adapters with custom indexes added using library preparation kits (KapaBiosystems, Woburn, MA), checked for quality, normalized, pooled, and run an Illumina MiSeq (paired-end 250 reads, Illumina Inc., San Diego, CA) at the Georgia Genomics Facility (University of Georgia). The read quality, trimming, and de novo assembly were performed using CLC Genomics Workbench 6.5 (CLC Bio, Boston, MA). The largest contig was used to annotate gene identity and position with different programs: DOGMA (Wyman et al., 2004), MITOS (Bernt et al., 2013), and MITOFISH (Iwasaki et al., 2013). The contig was compared with other 15 Actinopterygii full mitogenome sequences available in GenBank to resolve gene Correspondence: Francisco J. Garcı´a-De Leo´n, Laboratorio de Gene´tica para la Conservacio´n Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S. 23096, Me´xico. E-mail: [email protected]
inconsistencies, to determine the origin of replication and to infer phylogenetic relationships. The alignment and the Neighbor Joining phylogenetic tree were performed in Mega 6 (MEGA Inc., Englewood, NJ) (Tamura, et al. 2013). The length of the mitogenome of A. fimbria (Genbank accession KP777542) is 16,507 bp with a base composition of A 26.1%, C 29.6%, G 18.3%, and T 26%. The genome contains 11 genes encoding subunits of respiratory chain complexes (COX I– III, CYTB, ND subunits 1–6) and two genes encoding ATP synthase subunits. Genes are carried principally by heavy DNA strand, with the gene order ND1–ND2–COX1–COX2–ATP8– ATP6–COX3–ND3–ND4L–ND4–ND5–CYTB, and ND6 in the light strand. It also encodes 22 tRNAs and the 12S and 16S rRNAs subunits. The mitochondrial arrangement was similar to the sablefish’s mitogenome from Genbank (accession number JX070112.1). The genome varies in 118 positions present in 12S, tRNA-Val, 16S, ND 1-6, tRNA-Asn, COX1, ATP8, ATP6, COX3, and CYTB genes. The ND4 gene showed the highest number of differences, but only the ND2 presented an amino acid translation change from Valine to Isoleucine in the 4653–4655 position. The genetic distance between both mitogenomes of the sablefish was 0.7%. These differences support the hypothesis of at least two sablefish populations in the northeast Pacific (Tripp-Valdez et al., 2012). Although the phylogenetic tree showed that most nodes supported by high-bootstrap percentages, the phylogenetic position of the sablefish was unclear since it was placed as an ancestral node between two clear clades formed by Scorpaeniformes and Perciformes (Figure 1). Similar results were reported by Rondeau et al. (2013) so more information is needed in order to correctly classify the sablefish.
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/15/15 For personal use only.
2
C. Galva´n-Tirado et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Phylogenetic relationships among Actinopterygii sequences with the neighbor-joining method. Numbers at the nodes are bootstrap percentages. GenBank accession numbers: Anarhichas lupus (EF427916.1), Anarhichas minor (EF427917), Cottus czerskii (KJ956027.1), Cottus poecilopus (EU332750), Enophrys diceraus (KF039715.1), Gymnocephalus cernua (KM978956.1), Hexagrammos_agrammus (AB763992.1), Lycodes toyamensis (AP004448.1), Mesocottus haitej (KF170219.1), Pholis crassispina (AP004449), Pleurogrammus azonus (AB744047), Pleurogrammus_monopterygius (AB753026.1), Scaliscus amiscus (NC_004403), Sebastes schlegelii (AY491978), and Trachidermus fasciatus (JX017305.1).
Declaration of interest The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper. Funds were received from CIBNOR and CICESE through the SUBNARGENA and SAGARPA of Mexico and CONACYT Grant 2005-12058 to F. J. G. D. L.
References 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.
Rondeau, EB, Messmer AM, Sanderson DS, Jantzen SG, von Schalburg KR, Minkley DR, Leong JS, et al. (2013) Genomics of sablefish (Anoplopoma fimbria): Expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene. BMC Genom 14:452. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9. Tripp-Valdez MA, Garcı´a-De Leo´n FJ, Espinosa-Pe´rez H, Ruiz-Campos G. (2012) Population structure of sablefish Anoplopoma fimbria using genetic variability and geometric morphometric analysis. J Appl Ichthyol 28:516–23. Wyman SK, Jansen RK, Boore JL. (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
