http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.926487
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus Dean C. Blower1 and Jennifer R. Ovenden1,2 School of Biological Sciences, The University of Queensland, St. Lucia, Australia and 2Molecular Fisheries Laboratory, The University of Queensland, St. Lucia, Australia
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 10/11/14 For personal use only.
1
Abstract
Keywords
The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33 average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA’s, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.
454 sequencing, Carcharhinus plumbeus, de novo genome assembly, mitochondrial genome, genome annotation
The sandbar shark Carcharhinus plumbeus is a medium sized (approximately 2 metres total length) whaler shark (Last & Stevens, 2009). The distribution of C. plumbeus is widespread globally but discontinuous along the margins of continents from tropical to temperate regions waters (Last & Stevens, 2009). Carcharhinus plumbeus stocks in the western north Atlantic sustained very high fishing pressure for some years and are now considered overfished (IUCN Red List, 2009). Similarly, in Australian fisheries declining catch levels have prompted a reduction in catch quotas to negligible levels as a precautionary measure. The IUCN Red List considers C. plumbeus to be Vulnerable (Vulnerable A2bd + 4bd ver 3.1) to population depletion due to its low rates of increase and the steady exploitation that has led to declines (IUCN Red List, 2009). In this study a freshly caught (Tweed Heads, Australia) C. plumbeus was identified from morphological characteristics by a trained shark fisheries observer. Muscle tissue was excised and stored in 100% EtOH at 4 C. Extracted DNA was sequenced (ND4 gene region) genetically confirming the species as Carcharhinus plumbeus (Tillett et al., 2012). High molecular weight DNA submitted for a g picotitre plate of 454 pyrosequencing yielded 774,234 sequences with an average length of 672 basepairs (bp). Using Geneious Pro v6.0.5 (Drummond et al., 2011), 878 reads were mapped to the mitogenome scaffold of Carcharhinus obscurus (Blower et al., 2013) and assembled de novo producing a 16,706 bp mitochondrial genome assembly (Genbank Accession No.: KJ740750). The
History Received 22 April 2014 Revised 27 April 2014 Accepted 9 May 2014 Published online 18 June 2014
average depth of sequencing coverage was 33.4 (Min: 10.0, Max: 57.0, SD: 8.9) and roughly equal (17) in both forward and reverse directions. Mitogenome size and gene annotations showed concordance with those of other Carcharhiniformes [e.g. C. amblyrhynchoides (Feutry et al., 2014), C. falciformis (Galva´n-Tirado et al., 2014), C. leucus (Chen et al., 2014a), C. obscurus (Blower et al., 2013), and C. sorrah (Chen et al., 2014b)]. Structural components (Table 1) were as expected for a vertebrate mitogenome with 13 protein-coding regions (with only ND6 on the light strand), 22 tRNA genes (eight being on the light strand), 12S and 16S ribosomal RNAs, and two non-coding areas (origin of light strand replication (OL) and the control region). Protein folding structures predicted by MITOS (Bernt et al., 2013) matched the anticipated ‘‘clover leaf’’ conformation with the exception of heavy strand tRNASer, having a loop replacing the dihydrouridine arm. The overall mitogenome nucleotide proportions were A, 38.3%, T, 25.5%, G, 13.3%, C, 29.9%. As seen for other Carcharhiniformes, the complementary base composition was biased towards A–T (61.2%) relative to G–C (38.8%) content. The significant economic value and increasing conservation interest of this species and its family Carcharhinidae heightens the need for genetic research into forensic species identification, population and stock structure and molecular systematics. This mitochondrial genome facilitates these investigations which will assist in sustainable management of C. plumbeus populations.
Declaration of interest
Correspondence: Dean C. Blower, School of Biological Sciences, The University of Queensland, St. Lucia 4068, Australia. E-mail: [email protected]
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This works was supported by Fisheries Research and Development Corporation (FRDC) grant (2010/062) to Fisheries New South Wales (NSW) on behalf of the Australian Government, plus the NSW and Queensland governments.
2
D. C. Blower & J. R. Ovenden
Mitochondrial DNA, Early Online: 1–2
Table 1. Detailed structure of the Carcharhinus plumbeus mitochondrial genome. Position Locus
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 10/11/14 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX I tRNASer tRNAAsp COX II tRNALys ATP8 ATP6 COX III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt B tRNAThr tRNAPro D-loop
Codon
Strand
From
To
Length (bp)
H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L H
1 71 1027 1099 2772 2847 3822 3893 3964 4033 5078 5150 5219 5292 5327 5396 5466 7023 7097 7174 7865 7940 8098 8781 9569 9639 9988 10,058 10,348 11,729 11,798 11,865 11,937 13,762 14,284 14,356 15,501 15,575 15,644
70 1026 1098 2771 2846 3821 3891 3963 4032 5079 5148 5218 5291 5326 5394 5464 7022 7093 7166 7864 7938 8107 8781 9566 9638 9989 10,057 10,354 11,728 11,797 11,864 11,936 13,766 14,283 14,353 15,501 15,572 15,643 16,706
70 956 72 1673 75 975 70 71 69 1047 71 69 73 35 68 69 1557 71 70 691 74 168 684 786 70 351 70 297 1381 69 67 72 1830 522 70 1146 72 69 1063
References Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Blower DC, Hereward JP, Ovenden JR. (2013). The complete mitochondrial genome of the dusky shark Carcharhinus obscurus. Mitochondrial DNA 24:619–21. Chen X, Liu M, Peng Z, Shi X. (2014a). Mitochondrial genome of the bull shark Carcharhinus leucas (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. DOI: 10.3109/19401736.2013.855906. Chen X, Peng Z, Cai L, Xu Y. (2014b). Mitochondrial genome of the spottail shark Carcharhinus sorrah (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. DOI: 10.3109/19401736.2013.845764. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, et al. (2011). Geneious v6.0.5. Available: www.geneious.com (Accessed 5 June 2014).
Start
Stop
Anti-codon
Intragenic bases (bp)
GAA
0 0 0 0 0 0 0 +1 0 0 2 +1 0 0 0 +1 +1 0 +3 +7 0 +1 10 1 +2 0 2 0 7 0 0 0 0 5 0 +2 1 +2 0
TAC TAA ATG
TAA GAT TTG CAT
ATG
TAG TCA TGC GTT GCA GTA
GTG
TAA TGA GTC
ATG
T– –
ATG ATG ATG
TAA TAA TAA
ATG
TAG
ATG ATG
TAA T– –
TTT
TCC TCG GTG GCT TAG ATG ATG
TAA TAA
ATG
TAG
TTC TGT TGG
Feutry P, Pillans RD, Kyne PM, Chen X. (2014). Complete mitogenome of the Graceful Shark Carcharhinus amblyrhynchoides (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. DOI: 10.3109/19401736.2014.892094. Galva´n-Tirado C, Hinojosa-Alvarez S, Diaz-Jaimes P, Marcet-Houben M, Garcı´a-De-Leo´n FJ. (2014). The complete mitochondrial DNA of the silky shark (Carcharhinus falciformis). Mitochondrial DNA. DOI: 10.3109/19401736.2013.878922. Last PR, Stevens JD. (2009). Sharks and rays of Australia. 2nd ed. Melbourne: CSIRO Publishing. Tillett BJ, Field IC, Bradshaw CJA, Johnson G, Buckworth RC, Meekan MG, Ovenden JR. (2012). Accuracy of species identification by fisheries observers in a north Australian shark fishery. Fish Res 127: 109–15.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus Dean C. Blower1 and Jennifer R. Ovenden1,2 School of Biological Sciences, The University of Queensland, St. Lucia, Australia and 2Molecular Fisheries Laboratory, The University of Queensland, St. Lucia, Australia
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 10/11/14 For personal use only.
1
Abstract
Keywords
The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33 average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA’s, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.
454 sequencing, Carcharhinus plumbeus, de novo genome assembly, mitochondrial genome, genome annotation
The sandbar shark Carcharhinus plumbeus is a medium sized (approximately 2 metres total length) whaler shark (Last & Stevens, 2009). The distribution of C. plumbeus is widespread globally but discontinuous along the margins of continents from tropical to temperate regions waters (Last & Stevens, 2009). Carcharhinus plumbeus stocks in the western north Atlantic sustained very high fishing pressure for some years and are now considered overfished (IUCN Red List, 2009). Similarly, in Australian fisheries declining catch levels have prompted a reduction in catch quotas to negligible levels as a precautionary measure. The IUCN Red List considers C. plumbeus to be Vulnerable (Vulnerable A2bd + 4bd ver 3.1) to population depletion due to its low rates of increase and the steady exploitation that has led to declines (IUCN Red List, 2009). In this study a freshly caught (Tweed Heads, Australia) C. plumbeus was identified from morphological characteristics by a trained shark fisheries observer. Muscle tissue was excised and stored in 100% EtOH at 4 C. Extracted DNA was sequenced (ND4 gene region) genetically confirming the species as Carcharhinus plumbeus (Tillett et al., 2012). High molecular weight DNA submitted for a g picotitre plate of 454 pyrosequencing yielded 774,234 sequences with an average length of 672 basepairs (bp). Using Geneious Pro v6.0.5 (Drummond et al., 2011), 878 reads were mapped to the mitogenome scaffold of Carcharhinus obscurus (Blower et al., 2013) and assembled de novo producing a 16,706 bp mitochondrial genome assembly (Genbank Accession No.: KJ740750). The
History Received 22 April 2014 Revised 27 April 2014 Accepted 9 May 2014 Published online 18 June 2014
average depth of sequencing coverage was 33.4 (Min: 10.0, Max: 57.0, SD: 8.9) and roughly equal (17) in both forward and reverse directions. Mitogenome size and gene annotations showed concordance with those of other Carcharhiniformes [e.g. C. amblyrhynchoides (Feutry et al., 2014), C. falciformis (Galva´n-Tirado et al., 2014), C. leucus (Chen et al., 2014a), C. obscurus (Blower et al., 2013), and C. sorrah (Chen et al., 2014b)]. Structural components (Table 1) were as expected for a vertebrate mitogenome with 13 protein-coding regions (with only ND6 on the light strand), 22 tRNA genes (eight being on the light strand), 12S and 16S ribosomal RNAs, and two non-coding areas (origin of light strand replication (OL) and the control region). Protein folding structures predicted by MITOS (Bernt et al., 2013) matched the anticipated ‘‘clover leaf’’ conformation with the exception of heavy strand tRNASer, having a loop replacing the dihydrouridine arm. The overall mitogenome nucleotide proportions were A, 38.3%, T, 25.5%, G, 13.3%, C, 29.9%. As seen for other Carcharhiniformes, the complementary base composition was biased towards A–T (61.2%) relative to G–C (38.8%) content. The significant economic value and increasing conservation interest of this species and its family Carcharhinidae heightens the need for genetic research into forensic species identification, population and stock structure and molecular systematics. This mitochondrial genome facilitates these investigations which will assist in sustainable management of C. plumbeus populations.
Declaration of interest
Correspondence: Dean C. Blower, School of Biological Sciences, The University of Queensland, St. Lucia 4068, Australia. E-mail: [email protected]
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This works was supported by Fisheries Research and Development Corporation (FRDC) grant (2010/062) to Fisheries New South Wales (NSW) on behalf of the Australian Government, plus the NSW and Queensland governments.
2
D. C. Blower & J. R. Ovenden
Mitochondrial DNA, Early Online: 1–2
Table 1. Detailed structure of the Carcharhinus plumbeus mitochondrial genome. Position Locus
Mitochondrial DNA Downloaded from informahealthcare.com by UMEA University Library on 10/11/14 For personal use only.
Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COX I tRNASer tRNAAsp COX II tRNALys ATP8 ATP6 COX III tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt B tRNAThr tRNAPro D-loop
Codon
Strand
From
To
Length (bp)
H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H H L L H H L H
1 71 1027 1099 2772 2847 3822 3893 3964 4033 5078 5150 5219 5292 5327 5396 5466 7023 7097 7174 7865 7940 8098 8781 9569 9639 9988 10,058 10,348 11,729 11,798 11,865 11,937 13,762 14,284 14,356 15,501 15,575 15,644
70 1026 1098 2771 2846 3821 3891 3963 4032 5079 5148 5218 5291 5326 5394 5464 7022 7093 7166 7864 7938 8107 8781 9566 9638 9989 10,057 10,354 11,728 11,797 11,864 11,936 13,766 14,283 14,353 15,501 15,572 15,643 16,706
70 956 72 1673 75 975 70 71 69 1047 71 69 73 35 68 69 1557 71 70 691 74 168 684 786 70 351 70 297 1381 69 67 72 1830 522 70 1146 72 69 1063
References Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, et al. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol 69:313–19. Blower DC, Hereward JP, Ovenden JR. (2013). The complete mitochondrial genome of the dusky shark Carcharhinus obscurus. Mitochondrial DNA 24:619–21. Chen X, Liu M, Peng Z, Shi X. (2014a). Mitochondrial genome of the bull shark Carcharhinus leucas (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. DOI: 10.3109/19401736.2013.855906. Chen X, Peng Z, Cai L, Xu Y. (2014b). Mitochondrial genome of the spottail shark Carcharhinus sorrah (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. DOI: 10.3109/19401736.2013.845764. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, et al. (2011). Geneious v6.0.5. Available: www.geneious.com (Accessed 5 June 2014).
Start
Stop
Anti-codon
Intragenic bases (bp)
GAA
0 0 0 0 0 0 0 +1 0 0 2 +1 0 0 0 +1 +1 0 +3 +7 0 +1 10 1 +2 0 2 0 7 0 0 0 0 5 0 +2 1 +2 0
TAC TAA ATG
TAA GAT TTG CAT
ATG
TAG TCA TGC GTT GCA GTA
GTG
TAA TGA GTC
ATG
T– –
ATG ATG ATG
TAA TAA TAA
ATG
TAG
ATG ATG
TAA T– –
TTT
TCC TCG GTG GCT TAG ATG ATG
TAA TAA
ATG
TAG
TTC TGT TGG
Feutry P, Pillans RD, Kyne PM, Chen X. (2014). Complete mitogenome of the Graceful Shark Carcharhinus amblyrhynchoides (Carcharhiniformes: Carcharhinidae). Mitochondrial DNA. DOI: 10.3109/19401736.2014.892094. Galva´n-Tirado C, Hinojosa-Alvarez S, Diaz-Jaimes P, Marcet-Houben M, Garcı´a-De-Leo´n FJ. (2014). The complete mitochondrial DNA of the silky shark (Carcharhinus falciformis). Mitochondrial DNA. DOI: 10.3109/19401736.2013.878922. Last PR, Stevens JD. (2009). Sharks and rays of Australia. 2nd ed. Melbourne: CSIRO Publishing. Tillett BJ, Field IC, Bradshaw CJA, Johnson G, Buckworth RC, Meekan MG, Ovenden JR. (2012). Accuracy of species identification by fisheries observers in a north Australian shark fishery. Fish Res 127: 109–15.
