http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.878922
MITOGENOME ANNOUNCEMENT
The complete mitochondrial DNA of the silky shark (Carcharhinus falciformis) Carolina Galva´n-Tirado1, Silvia Hinojosa-Alvarez1, Pindaro Diaz-Jaimes1, Marina Marcet-Houben2 and Francisco J. Garcı´a-De-Leo´n3
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 06/20/14 For personal use only.
1
Laboratorio de Gene´tica de Organismos Acua´ticos, Instituto de Ciencias del Mar y Limnologı´a, Ciudad Universitaria, Me´xico DF, 2Bioinformatics Programme, Centre de Regulacio´Geno`mica (CRG-UPF), Barcelona, Spain, and 3Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, La Paz, Me´xico
Abstract
Keywords
The silky shark mitogenome (GeneBank accession number KF801102) has a total length of 17,774 bp, the base composition of the genomes was as follows: A (31.36%), T (30.18%), C (25.27%) and G (13.17%), which demonstrated an A + T-rich feature (61.64%), similar to other elasmobranch mitogenomes. The mitochondrial genome contained 13 protein-coding genes and 23 tRNA genes. The tRNA genes ranged from 70 to 72 bp. The gene order was the same as in other vertebrates and teleosts.
Carcharhinus falciformis, elasmobranchs, mitochondrial DNA
The silky shark is a common tropical-subtropical species that occurs in the Atlantic, Pacific and Indian oceans (Compagno, 1984). Due to its abundance, it is considered important for longline and gillnet fisheries in the Gulf of Mexico, Caribbean, Maldives, Sri Lanka, Japanese waters and mid-Atlantic coasts of the United States (Roma´n-Verdesoto & Orozco-Zo¨ller, 2005). Similar to other carcharhinids, the silky shark is vulnerable to over-fishing due to its long gestation periods and slow growth rate (Bonfil et al., 2009). The IUCN has listed silky shark as ‘‘Least Concern’’; however, this category is given because neither its population status nor its key biological aspects have been assessed. We sequenced the complete mitochondrial genome of the silky shark (GeneBank accession number KF801102) from a specimen collected in the Eastern Pacific, whose biopsy has been deposited in the Laboratorio de Organismos Acua´ticos, Instituto de Ciencias del Mar y Limnologı´a (ICMyL) de la Universidad Auto´noma de Me´xico (UNAM). The DNA was sheared using Covaris and Illumina adapters that were ligated, the libraries were controlled for quality, normalized, poole, and run on a MiSeq v2 500 cycle kit (Illumina, Inc., San Diego, CA) to produce paired-end 250 nt reads. Sequences were assembled using SOAP de novo (Li et al., 2010), and contigs belonging to the mtDNA were selected. Annotation of the assembled mitogenome was performed using DOGMA (Wyman et al., 2004). The silky shark mitochondrial structure was similar to that of other elasmobranchs such as the dusky shark, Carcharhinus obscurus (Blower et al., 2013). The silky shark mitogenome has
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., Me´xico. E-mail: [email protected]
History Received 16 December 2013 Accepted 18 December 2013 Published online 22 January 2014
a total length of 17,774 bp, and the base composition of the genomes was as follows: A (31.36%), T (30.18%), C (25.27%) and G (13.17%), which demonstrated an A + T-reich feature (61.64%), similar to other elasmobranch mitogenomes. The mitochondrial genome contained 13 protein-coding genes and 23 tRNA genes. The tRNA genes ranged from 70 to 72 bp. The gene order is the Table 1. Mitogenome gene order of the silky shark (C. falciformis).
Start 1063 1136 2089 2161 3947 4022 4997 5068 5139 5208 6252 6253 6325 6394 6502 6571 6641 8198 8272 8349 9040 9115 9273 10,040
End
Gene Name
Lenght (bp)
1132 2084 2160 3946 4021 4993 5066 5139 5207 6245 6322 6323 6393 6466 6569 6639 8194 8268 8341 9038 9113 9279 10,037 10,822
tRNA-Phe 12sRNA tRNA-Val 16sRNA tRNA-Leu ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Ser tRNA-Trp tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr COI tRNA-Ser tRNA-Asp COX2 tRNA-Leu ATPase8 ATPase6 COX3
69 948 71 1785 74 971 69 71 68 1037 70 70 68 72 67 68 1553 70 69 689 73 164 764 782 (continued )
2
C. Galva´n-Tirado et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Start
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 06/20/14 For personal use only.
10,828 10,898 11,247 11,317 11,607 12,984 12,988 13,057 13,124 13,196 15,010 15,484 15,556 16,701 16,775 16,644
End
Gene Name
Lenght (bp)
10,897 11,245 11,316 11,610 12,986 13,058 13,056 13,123 13,195 15,013 15,483 15,553 16,698 16,772 16,843 17,774
tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-Phe tRNA-His tRNA-Ser tRNA-Leu ND5 ND6 tRNA-Glu CYTB tRNA-Thr tRNA-Pro Control region
69 347 69 293 1379 74 68 66 71 1817 473 69 1142 71 68 1066
same as in other vertebrates and teleosts (Table 1). This new mitochondrial genome will provide useful information for subsequent phylogenetic and population analyses in the genus Carcharhinus.
Acknowledgements Thanks to Travis Glen for support in next generation sequencing.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and composition of the paper.
References Blower DC, Hereward JP, Ovenden JR. (2013). The complete mitochondrialgenome of the dusky shark Carcharhinus obscurus. Mitochondrial DNA 24:619–21. Bonfil R, Amorim A, Anderson C, Arauz R, Baum J, Clarke SC, Graham RT, et al. (2009). Carcharhinus falciformis. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.2. Available at: http:// www.iucnredlist.org/apps/redlist/details/39370/0 (Accessed 15 November 2011). Compagno LJV. (1984). FAO species catalogue. Vol. 4. Sharks of the world. An annotated and illustrated catalogue of shark species known to date. Part 2. Carcharhiniformes. FAO Fisheries Synopis (125). Rome, Italy: FAO. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, et al. (2010). The sequence and de novo assembly of the giant panda genome. Nature 463:311–17. Roma´n-Verdesoto M, Orozco-Zo¨ller M. (2005). Bycatches of sharks in the tuna purse-seine fishery of the eastern Pacific Ocean reported by observers of the Inter-American Tropical Tuna Commission, 1993–2004. Data report 11. La Jolla, CA. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial DNA of the silky shark (Carcharhinus falciformis) Carolina Galva´n-Tirado1, Silvia Hinojosa-Alvarez1, Pindaro Diaz-Jaimes1, Marina Marcet-Houben2 and Francisco J. Garcı´a-De-Leo´n3
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 06/20/14 For personal use only.
1
Laboratorio de Gene´tica de Organismos Acua´ticos, Instituto de Ciencias del Mar y Limnologı´a, Ciudad Universitaria, Me´xico DF, 2Bioinformatics Programme, Centre de Regulacio´Geno`mica (CRG-UPF), Barcelona, Spain, and 3Laboratorio de Gene´tica para la Conservacio´n, Centro de Investigaciones Biolo´gicas del Noroeste, Instituto Polite´cnico Nacional 195, La Paz, Me´xico
Abstract
Keywords
The silky shark mitogenome (GeneBank accession number KF801102) has a total length of 17,774 bp, the base composition of the genomes was as follows: A (31.36%), T (30.18%), C (25.27%) and G (13.17%), which demonstrated an A + T-rich feature (61.64%), similar to other elasmobranch mitogenomes. The mitochondrial genome contained 13 protein-coding genes and 23 tRNA genes. The tRNA genes ranged from 70 to 72 bp. The gene order was the same as in other vertebrates and teleosts.
Carcharhinus falciformis, elasmobranchs, mitochondrial DNA
The silky shark is a common tropical-subtropical species that occurs in the Atlantic, Pacific and Indian oceans (Compagno, 1984). Due to its abundance, it is considered important for longline and gillnet fisheries in the Gulf of Mexico, Caribbean, Maldives, Sri Lanka, Japanese waters and mid-Atlantic coasts of the United States (Roma´n-Verdesoto & Orozco-Zo¨ller, 2005). Similar to other carcharhinids, the silky shark is vulnerable to over-fishing due to its long gestation periods and slow growth rate (Bonfil et al., 2009). The IUCN has listed silky shark as ‘‘Least Concern’’; however, this category is given because neither its population status nor its key biological aspects have been assessed. We sequenced the complete mitochondrial genome of the silky shark (GeneBank accession number KF801102) from a specimen collected in the Eastern Pacific, whose biopsy has been deposited in the Laboratorio de Organismos Acua´ticos, Instituto de Ciencias del Mar y Limnologı´a (ICMyL) de la Universidad Auto´noma de Me´xico (UNAM). The DNA was sheared using Covaris and Illumina adapters that were ligated, the libraries were controlled for quality, normalized, poole, and run on a MiSeq v2 500 cycle kit (Illumina, Inc., San Diego, CA) to produce paired-end 250 nt reads. Sequences were assembled using SOAP de novo (Li et al., 2010), and contigs belonging to the mtDNA were selected. Annotation of the assembled mitogenome was performed using DOGMA (Wyman et al., 2004). The silky shark mitochondrial structure was similar to that of other elasmobranchs such as the dusky shark, Carcharhinus obscurus (Blower et al., 2013). The silky shark mitogenome has
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., Me´xico. E-mail: [email protected]
History Received 16 December 2013 Accepted 18 December 2013 Published online 22 January 2014
a total length of 17,774 bp, and the base composition of the genomes was as follows: A (31.36%), T (30.18%), C (25.27%) and G (13.17%), which demonstrated an A + T-reich feature (61.64%), similar to other elasmobranch mitogenomes. The mitochondrial genome contained 13 protein-coding genes and 23 tRNA genes. The tRNA genes ranged from 70 to 72 bp. The gene order is the Table 1. Mitogenome gene order of the silky shark (C. falciformis).
Start 1063 1136 2089 2161 3947 4022 4997 5068 5139 5208 6252 6253 6325 6394 6502 6571 6641 8198 8272 8349 9040 9115 9273 10,040
End
Gene Name
Lenght (bp)
1132 2084 2160 3946 4021 4993 5066 5139 5207 6245 6322 6323 6393 6466 6569 6639 8194 8268 8341 9038 9113 9279 10,037 10,822
tRNA-Phe 12sRNA tRNA-Val 16sRNA tRNA-Leu ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Ser tRNA-Trp tRNA-Ala tRNA-Asn tRNA-Cys tRNA-Tyr COI tRNA-Ser tRNA-Asp COX2 tRNA-Leu ATPase8 ATPase6 COX3
69 948 71 1785 74 971 69 71 68 1037 70 70 68 72 67 68 1553 70 69 689 73 164 764 782 (continued )
2
C. Galva´n-Tirado et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Start
Mitochondrial DNA Downloaded from informahealthcare.com by University of Laval on 06/20/14 For personal use only.
10,828 10,898 11,247 11,317 11,607 12,984 12,988 13,057 13,124 13,196 15,010 15,484 15,556 16,701 16,775 16,644
End
Gene Name
Lenght (bp)
10,897 11,245 11,316 11,610 12,986 13,058 13,056 13,123 13,195 15,013 15,483 15,553 16,698 16,772 16,843 17,774
tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-Phe tRNA-His tRNA-Ser tRNA-Leu ND5 ND6 tRNA-Glu CYTB tRNA-Thr tRNA-Pro Control region
69 347 69 293 1379 74 68 66 71 1817 473 69 1142 71 68 1066
same as in other vertebrates and teleosts (Table 1). This new mitochondrial genome will provide useful information for subsequent phylogenetic and population analyses in the genus Carcharhinus.
Acknowledgements Thanks to Travis Glen for support in next generation sequencing.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and composition of the paper.
References Blower DC, Hereward JP, Ovenden JR. (2013). The complete mitochondrialgenome of the dusky shark Carcharhinus obscurus. Mitochondrial DNA 24:619–21. Bonfil R, Amorim A, Anderson C, Arauz R, Baum J, Clarke SC, Graham RT, et al. (2009). Carcharhinus falciformis. In: IUCN 2011. IUCN Red List of Threatened Species. Version 2011.2. Available at: http:// www.iucnredlist.org/apps/redlist/details/39370/0 (Accessed 15 November 2011). Compagno LJV. (1984). FAO species catalogue. Vol. 4. Sharks of the world. An annotated and illustrated catalogue of shark species known to date. Part 2. Carcharhiniformes. FAO Fisheries Synopis (125). Rome, Italy: FAO. Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, et al. (2010). The sequence and de novo assembly of the giant panda genome. Nature 463:311–17. Roma´n-Verdesoto M, Orozco-Zo¨ller M. (2005). Bycatches of sharks in the tuna purse-seine fishery of the eastern Pacific Ocean reported by observers of the Inter-American Tropical Tuna Commission, 1993–2004. Data report 11. La Jolla, CA. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5.
