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 genome of the deep-sea stony coral Solenosmilia variabilis (Scleractinia, Caryophylliidae) and its interindividual variation Cong Zeng, Di M. Tracey, Malcolm R. Clark, Ashley A. Rowden, Leighton J. Thomas & Jonathan P. A. Gardner To cite this article: Cong Zeng, Di M. Tracey, Malcolm R. Clark, Ashley A. Rowden, Leighton J. Thomas & Jonathan P. A. Gardner (2014): The complete mitochondrial genome of the deepsea stony coral Solenosmilia variabilis (Scleractinia, Caryophylliidae) and its inter-individual variation, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971306
Published online: 20 Oct 2014.
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Date: 05 November 2015, At: 18:08
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971306
MITOGENOME ANNOUNCEMENTS
The complete mitochondrial genome of the deep-sea stony coral Solenosmilia variabilis (Scleractinia, Caryophylliidae) and its inter-individual variation Cong Zeng1, Di M. Tracey2, Malcolm R. Clark2, Ashley A. Rowden,2 Leighton J. Thomas1, and Jonathan P. A. Gardner1
Downloaded by [Deakin University Library] at 18:08 05 November 2015
1
School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand and 2National Institute of Water and Atmospheric Research Limited, Wellington, New Zealand Abstract
Keywords
Three individual-specific DNA libraries of the deep-sea scleractinian coral Solenosmilia variabilis (Duncan, 1873) were constructed to obtain complete mitochondrial genomes using the 454 Life Science pyrosequencing system. Two mitogenomes were successfully assembled: both were 15,968 bp in length, with base composition of A (24.2%), T (41.1%), C (13.7%) and G (21.0%). The genome contains 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a D-loop region. The two mitogenomes were almost identical, with only 5 nucleotide differences (0.03%), including a synonymous substitution within the nad1, nad2 and nad4L genes, and two transversions in the D-loop region. This inter-individual variation indicates that these genes and/or region are potential candidates as molecular markers for population genetic research. The mitogenome of S. variabilis will be useful for future phylogenetic and phylogeographic studies of deep-sea corals.
Deep sea, mitogenome, Scleractinia, Solenosmilia variabilis
Solenosmilia variabilis (Duncan, 1873) (Order: Scleractinia) is a deep-sea coral that is globally distributed (Davies & Guinotte, 2011), and often found on seamounts (Tracey et al., 2011). With its complex matrix-like growth structure, S. variabilis can form ‘‘reefs’’. Such habitat can support invertebrate and fish assemblages with relatively high species richness (Henry & Roberts, 2007). The stony coral reef habitat is fragile and easily damaged by near-bottom trawling (Clark & Rowden, 2009), and is potentially vulnerable to the effects of climate change and ocean acidification (Fallon et al., 2014). Habitat formed by stony corals such as S. variabilis are considered vulnerable marine ecosystems (VMEs) (FAO, 2009), and included as one of ten VME indicator taxa in the South Pacific Ocean (Parker et al., 2009). Three S. variabilis specimens were collected, one from Anvil Seamount (37.707 S, 169.015 E) and two from Valerie Guyot (41.581 S, 164.255 E and 41.364 S, 164.419 E). The seamount and guyot are 500 km apart on the Louisville Seamount Chain, to the east of New Zealand’s Exclusive Economic Zone in the South Pacific Ocean (Clark et al., 2014). DNA was extracted from branch sections bearing polyps using guanidinium thiocyanate (Boom et al., 1990). Three individual-specific barcoded DNA libraries were sequenced on a 454 GS FLX sequencer (Macrogen, Korea). Following Elbrecht et al. (2013), the mitogenome of Lophelia pertusa (GenBank No. KC875349, Flot et al., 2013), with the highest pairwise identity on COI region, was used to identify DNA sequences and extract all mitogenome reads from
Correspondence: Cong Zeng, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand. E-mail: [email protected]
History Received 24 September 2014 Accepted 26 September 2014 Published online 20 October 2014
the S. variabilis libraries using the discontinuous megablast algorithm BLASTn in the Geneious software package (max e-values 1e-20) (Drummond et al., 2013). Extracted reads were assembled by mapping to the reference mitogenome of L. pertusa. The first draft genome was manually checked and then used as a search query to identify additional reads in the 454 read database. The mitogenome was annotated for Coding DNA Sequence (CDS), tRNA and rRNA by comparison with all available scleractinian mitogenomes in GenBank (n ¼ 30). The ORFs finder and Annotation (Invertebrate Mitochondrial) functions in Geneious were used to check the position, start and stop codons and length of each CDS. The same method was applied to construct three mitochondrial genomes from the three libraries but using the mitogenome constructed above as the reference. After assembling the mitogenomes from three libraries, multiple alignment (ClustalW) was utilized to compare differences among the three mitogenomes in Geneious. The first assembled draft contained 506 reads from pooled three databases, with good overall coverage (minimum coverage was 7 sequences, maximum coverage was 38 sequences, average coverage was 22.0 (SD ¼ 6.8)). Having assembled all relevant reads from each library, two S. variabilis mitogenomes were successfully obtained, one from Anvil Seamount and one from Valerie Guyot. The two mitogenomes were almost identical, the length of both being 15,968 bp. Both mitochondrial genomes included 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a D-loop region (Table 1). The base composition of the genome was A (24.2%), T (41.1%), C (13.7%) and G (21.0%). There were 5 nucleotide differences (0.03%) between the two mitogenomes, including synonymous substitutions in the genes nad1, nad4L and nad2 (at 1276 bp, 6596 bp and 10,502 bp, respectively) and two 1 bp differences (G/T
2
C. Zeng et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characterization of the mitochondrial genome of Solenosmilia variabilis. Name
Downloaded by [Deakin University Library] at 18:08 05 November 2015
nad5 nad5 intron nad1 atp6 nad4 12S rRNA COIII COII nad4L nad3
Location 50 -30
Size (bp)
Start
Stop
Name
Location 50 -30
Size (bp)
1–8295 715–7173 824–1771 1824–2522 2522–3967 3968–4991 4992–5771 5759–6484 6474–6773 6775–7119
1836 6459 948 699 1446 1023 780 726 300 345
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATG GTG ATG ATG
TAG TAA TAA TAA
D-loop cytb nad2 nad6 tRNA-Trp atp8 COI tRNA-Met 16S rRNA
8296–8818 8819–9979 9975–11,291 11,293–11,847 12,250–12,319 12,323–12,490 12,480–14,045 14,041–14,111 14,112–15,968
523 1161 1317 555 70 168 1566 71 1857
transversions at 8701 and 8768 bp) in the D-loop region. The annotated mitogenomes are available online in NCBI (GenBank accession numbers KM609293 and KM609294). The full mitochondrial genome of S. variabilis, at 15,968 bp, was slightly shorter than that of a branching habitat-forming species not found in the New Zealand region, L. pertusa (16,149 bp). The small difference between the species is primarily due to a 186 bp deletion in the D-loop region. The number and order of predicted genes in the S. variabilis mitogenome were identical to L. pertusa, and the pairwise sequence identity between the two taxa was 97.5%. Although unable to assemble the third full mitogenome, we found no differences in the D-loop region between the two specimens from Valerie Guyot, suggesting that genetic variation in the mitochondrial genome is low. Similarly, limited genetic differences in the mitogenomes of two L. pertusa collected from the Mediterranean and Barents seas had been reported, which differed only at a single non-synonymous substitution (Flot et al., 2013). The variation information of the mitogenome will be beneficial for future phylogenetic and phylogeographic studies of Scleractinia, particularly for S. variabilis, and useful where there may be some confusion with specimen identification.
Acknowledgements Samples were collected by NIWA using an epibenthic sled during the Louisville Seamount Chain voyage (TAN1402). We thank the scientists and crew of voyage TAN1402 who collected the coral specimens. We are grateful to Sadie Mills and Kareen Schnabel (NIWA Invertebrate Collection), for their diligent assistance with specimen samples.
Declaration of interest This study was supported by funding from the New Zealand Ministry of Business, Innovation and Employment. The voyage was part of the South Pacific Vulnerable Marine Ecosystems Project funded by the New Zealand Ministry of Business, Innovation & Employment (C01X1229), and was also supported by the New Zealand Ministry for Primary Industries. This research was also funded by NIWA under Coasts and Oceans Research Programme 2 Marine Biological Resources: Discovery and definition of the marine biota of New Zealand (2014/2015 SCI).
Start
Stop
ATG ATT GTG
TAG TAA TAA
ATG ATG
TAA TAA
References Boom RCJA, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, Van der Noordaa JPME. (1990). Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28:495–503. Clark MR, Rowden AA. (2009). Effect of deepwater trawling on the macro-invertebrate assemblages of seamounts on the Chatham Rise, New Zealand. Deep-Sea Res I 56:1540–4. Clark MR, Anderson O, Bowden D, Chin C, George S, Glasgow D, Guinotte J, et al. (2014). Vulnerable Marine Ecosystems on the Louisville Seamount Chain: Voyage report of a survey (TAN1402) in February 2014. New Zealand Aquatic Environment and Biodiversity Report. Available at: http://www.deepwater.co.nz/wp-content/uploads/ 2014/07/Clark-et-al.-2014-Voyage-Report-of-a-Survey-of-Deep-SeaHabitats-of-the-Louisville-Seamount-Chain-Tan1402.-PreliminaryProject-report-VMES133.-May-2014.-84p.pdf. Davies AJ, Guinotte JM. (2011). Global habitat suitability for frameworkforming cold-water corals. PLoS One 6:e18483. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, et al. (2013). Geneious v7.0.5. Available at: http:// www.geneious.com/ Elbrecht V, Poettker L, John U, Leese F. (2013). The complete mitochondrial genome of the stonefly Dinocras cephalotes (Plecoptera, Perlidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.830301. Fallon SJ, Thresher RE, Adkins J. (2014). Age and growth of the coldwater scleractinian Solenosmilia variabilis and its reef on SW Pacific seamounts. Coral Reefs 33:31–8. FAO. (2009). International Guidelines for the Management of Deep-Sea Fisheries in the High-Seas. Rome, Italy: Food and Agriculture Organisation of the United Nations. 73 p. Flot JF, Dahl M, Andre´ C. (2013). Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences. BMC Res Notes 6:144. Henry LA, Roberts JM. (2007). Biodiversity and ecological composition of macrobenthos on cold-water coral mounds and adjacent offmound habitat in the bathyal Porcupine Seabight, NE Atlantic. Deep-Sea Res I 54:654–72. Parker, SJ, Penney AJ, Clark MR. (2009). Detection criteria for managing trawl impacts on vulnerable marine ecosystems in high seas fisheries of the South Pacific Ocean. Marine Ecol Prog Series 397: 309–17. Tracey DM, Rowden AA, Mackay KA, Compton T. (2011). Habitatforming cold-water corals show affinity for seamounts in the New Zealand region. Marine Ecol Prog Series 430:1–22.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of the deep-sea stony coral Solenosmilia variabilis (Scleractinia, Caryophylliidae) and its interindividual variation Cong Zeng, Di M. Tracey, Malcolm R. Clark, Ashley A. Rowden, Leighton J. Thomas & Jonathan P. A. Gardner To cite this article: Cong Zeng, Di M. Tracey, Malcolm R. Clark, Ashley A. Rowden, Leighton J. Thomas & Jonathan P. A. Gardner (2014): The complete mitochondrial genome of the deepsea stony coral Solenosmilia variabilis (Scleractinia, Caryophylliidae) and its inter-individual variation, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971306
Published online: 20 Oct 2014.
Submit your article to this journal
Article views: 18
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: [Deakin University Library]
Date: 05 November 2015, At: 18:08
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971306
MITOGENOME ANNOUNCEMENTS
The complete mitochondrial genome of the deep-sea stony coral Solenosmilia variabilis (Scleractinia, Caryophylliidae) and its inter-individual variation Cong Zeng1, Di M. Tracey2, Malcolm R. Clark2, Ashley A. Rowden,2 Leighton J. Thomas1, and Jonathan P. A. Gardner1
Downloaded by [Deakin University Library] at 18:08 05 November 2015
1
School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand and 2National Institute of Water and Atmospheric Research Limited, Wellington, New Zealand Abstract
Keywords
Three individual-specific DNA libraries of the deep-sea scleractinian coral Solenosmilia variabilis (Duncan, 1873) were constructed to obtain complete mitochondrial genomes using the 454 Life Science pyrosequencing system. Two mitogenomes were successfully assembled: both were 15,968 bp in length, with base composition of A (24.2%), T (41.1%), C (13.7%) and G (21.0%). The genome contains 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a D-loop region. The two mitogenomes were almost identical, with only 5 nucleotide differences (0.03%), including a synonymous substitution within the nad1, nad2 and nad4L genes, and two transversions in the D-loop region. This inter-individual variation indicates that these genes and/or region are potential candidates as molecular markers for population genetic research. The mitogenome of S. variabilis will be useful for future phylogenetic and phylogeographic studies of deep-sea corals.
Deep sea, mitogenome, Scleractinia, Solenosmilia variabilis
Solenosmilia variabilis (Duncan, 1873) (Order: Scleractinia) is a deep-sea coral that is globally distributed (Davies & Guinotte, 2011), and often found on seamounts (Tracey et al., 2011). With its complex matrix-like growth structure, S. variabilis can form ‘‘reefs’’. Such habitat can support invertebrate and fish assemblages with relatively high species richness (Henry & Roberts, 2007). The stony coral reef habitat is fragile and easily damaged by near-bottom trawling (Clark & Rowden, 2009), and is potentially vulnerable to the effects of climate change and ocean acidification (Fallon et al., 2014). Habitat formed by stony corals such as S. variabilis are considered vulnerable marine ecosystems (VMEs) (FAO, 2009), and included as one of ten VME indicator taxa in the South Pacific Ocean (Parker et al., 2009). Three S. variabilis specimens were collected, one from Anvil Seamount (37.707 S, 169.015 E) and two from Valerie Guyot (41.581 S, 164.255 E and 41.364 S, 164.419 E). The seamount and guyot are 500 km apart on the Louisville Seamount Chain, to the east of New Zealand’s Exclusive Economic Zone in the South Pacific Ocean (Clark et al., 2014). DNA was extracted from branch sections bearing polyps using guanidinium thiocyanate (Boom et al., 1990). Three individual-specific barcoded DNA libraries were sequenced on a 454 GS FLX sequencer (Macrogen, Korea). Following Elbrecht et al. (2013), the mitogenome of Lophelia pertusa (GenBank No. KC875349, Flot et al., 2013), with the highest pairwise identity on COI region, was used to identify DNA sequences and extract all mitogenome reads from
Correspondence: Cong Zeng, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand. E-mail: [email protected]
History Received 24 September 2014 Accepted 26 September 2014 Published online 20 October 2014
the S. variabilis libraries using the discontinuous megablast algorithm BLASTn in the Geneious software package (max e-values 1e-20) (Drummond et al., 2013). Extracted reads were assembled by mapping to the reference mitogenome of L. pertusa. The first draft genome was manually checked and then used as a search query to identify additional reads in the 454 read database. The mitogenome was annotated for Coding DNA Sequence (CDS), tRNA and rRNA by comparison with all available scleractinian mitogenomes in GenBank (n ¼ 30). The ORFs finder and Annotation (Invertebrate Mitochondrial) functions in Geneious were used to check the position, start and stop codons and length of each CDS. The same method was applied to construct three mitochondrial genomes from the three libraries but using the mitogenome constructed above as the reference. After assembling the mitogenomes from three libraries, multiple alignment (ClustalW) was utilized to compare differences among the three mitogenomes in Geneious. The first assembled draft contained 506 reads from pooled three databases, with good overall coverage (minimum coverage was 7 sequences, maximum coverage was 38 sequences, average coverage was 22.0 (SD ¼ 6.8)). Having assembled all relevant reads from each library, two S. variabilis mitogenomes were successfully obtained, one from Anvil Seamount and one from Valerie Guyot. The two mitogenomes were almost identical, the length of both being 15,968 bp. Both mitochondrial genomes included 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a D-loop region (Table 1). The base composition of the genome was A (24.2%), T (41.1%), C (13.7%) and G (21.0%). There were 5 nucleotide differences (0.03%) between the two mitogenomes, including synonymous substitutions in the genes nad1, nad4L and nad2 (at 1276 bp, 6596 bp and 10,502 bp, respectively) and two 1 bp differences (G/T
2
C. Zeng et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characterization of the mitochondrial genome of Solenosmilia variabilis. Name
Downloaded by [Deakin University Library] at 18:08 05 November 2015
nad5 nad5 intron nad1 atp6 nad4 12S rRNA COIII COII nad4L nad3
Location 50 -30
Size (bp)
Start
Stop
Name
Location 50 -30
Size (bp)
1–8295 715–7173 824–1771 1824–2522 2522–3967 3968–4991 4992–5771 5759–6484 6474–6773 6775–7119
1836 6459 948 699 1446 1023 780 726 300 345
ATG
TAA
ATG ATG ATG
TAA TAA TAG
ATG GTG ATG ATG
TAG TAA TAA TAA
D-loop cytb nad2 nad6 tRNA-Trp atp8 COI tRNA-Met 16S rRNA
8296–8818 8819–9979 9975–11,291 11,293–11,847 12,250–12,319 12,323–12,490 12,480–14,045 14,041–14,111 14,112–15,968
523 1161 1317 555 70 168 1566 71 1857
transversions at 8701 and 8768 bp) in the D-loop region. The annotated mitogenomes are available online in NCBI (GenBank accession numbers KM609293 and KM609294). The full mitochondrial genome of S. variabilis, at 15,968 bp, was slightly shorter than that of a branching habitat-forming species not found in the New Zealand region, L. pertusa (16,149 bp). The small difference between the species is primarily due to a 186 bp deletion in the D-loop region. The number and order of predicted genes in the S. variabilis mitogenome were identical to L. pertusa, and the pairwise sequence identity between the two taxa was 97.5%. Although unable to assemble the third full mitogenome, we found no differences in the D-loop region between the two specimens from Valerie Guyot, suggesting that genetic variation in the mitochondrial genome is low. Similarly, limited genetic differences in the mitogenomes of two L. pertusa collected from the Mediterranean and Barents seas had been reported, which differed only at a single non-synonymous substitution (Flot et al., 2013). The variation information of the mitogenome will be beneficial for future phylogenetic and phylogeographic studies of Scleractinia, particularly for S. variabilis, and useful where there may be some confusion with specimen identification.
Acknowledgements Samples were collected by NIWA using an epibenthic sled during the Louisville Seamount Chain voyage (TAN1402). We thank the scientists and crew of voyage TAN1402 who collected the coral specimens. We are grateful to Sadie Mills and Kareen Schnabel (NIWA Invertebrate Collection), for their diligent assistance with specimen samples.
Declaration of interest This study was supported by funding from the New Zealand Ministry of Business, Innovation and Employment. The voyage was part of the South Pacific Vulnerable Marine Ecosystems Project funded by the New Zealand Ministry of Business, Innovation & Employment (C01X1229), and was also supported by the New Zealand Ministry for Primary Industries. This research was also funded by NIWA under Coasts and Oceans Research Programme 2 Marine Biological Resources: Discovery and definition of the marine biota of New Zealand (2014/2015 SCI).
Start
Stop
ATG ATT GTG
TAG TAA TAA
ATG ATG
TAA TAA
References Boom RCJA, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, Van der Noordaa JPME. (1990). Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28:495–503. Clark MR, Rowden AA. (2009). Effect of deepwater trawling on the macro-invertebrate assemblages of seamounts on the Chatham Rise, New Zealand. Deep-Sea Res I 56:1540–4. Clark MR, Anderson O, Bowden D, Chin C, George S, Glasgow D, Guinotte J, et al. (2014). Vulnerable Marine Ecosystems on the Louisville Seamount Chain: Voyage report of a survey (TAN1402) in February 2014. New Zealand Aquatic Environment and Biodiversity Report. Available at: http://www.deepwater.co.nz/wp-content/uploads/ 2014/07/Clark-et-al.-2014-Voyage-Report-of-a-Survey-of-Deep-SeaHabitats-of-the-Louisville-Seamount-Chain-Tan1402.-PreliminaryProject-report-VMES133.-May-2014.-84p.pdf. Davies AJ, Guinotte JM. (2011). Global habitat suitability for frameworkforming cold-water corals. PLoS One 6:e18483. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, et al. (2013). Geneious v7.0.5. Available at: http:// www.geneious.com/ Elbrecht V, Poettker L, John U, Leese F. (2013). The complete mitochondrial genome of the stonefly Dinocras cephalotes (Plecoptera, Perlidae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2013.830301. Fallon SJ, Thresher RE, Adkins J. (2014). Age and growth of the coldwater scleractinian Solenosmilia variabilis and its reef on SW Pacific seamounts. Coral Reefs 33:31–8. FAO. (2009). International Guidelines for the Management of Deep-Sea Fisheries in the High-Seas. Rome, Italy: Food and Agriculture Organisation of the United Nations. 73 p. Flot JF, Dahl M, Andre´ C. (2013). Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences. BMC Res Notes 6:144. Henry LA, Roberts JM. (2007). Biodiversity and ecological composition of macrobenthos on cold-water coral mounds and adjacent offmound habitat in the bathyal Porcupine Seabight, NE Atlantic. Deep-Sea Res I 54:654–72. Parker, SJ, Penney AJ, Clark MR. (2009). Detection criteria for managing trawl impacts on vulnerable marine ecosystems in high seas fisheries of the South Pacific Ocean. Marine Ecol Prog Series 397: 309–17. Tracey DM, Rowden AA, Mackay KA, Compton T. (2011). Habitatforming cold-water corals show affinity for seamounts in the New Zealand region. Marine Ecol Prog Series 430:1–22.
