Complete mitochondrial genome of the endangered Mary River turtle (Elusor macrurus) and low mtDNA variation across the species’ range
Daniel J. Schmidt A D , Brittany Brockett A , Thomas Espinoza B , Marilyn Connell C and Jane M. Hughes A
+ Author Affiliations
- Author Affiliations
A Australian Rivers Institute, Griffith University, Nathan, Qld 4111, Australia.
B Queensland Department of Natural Resources and Mines, Bundaberg, Qld 4670, Australia.
C Tiaro and District Landcare Group, Tiaro, Qld 4650, Australia.
D Corresponding author. Email: d.schmidt@griffith.edu.au
Australian Journal of Zoology 64(2) 117-121 https://doi.org/10.1071/ZO16013
Submitted: 26 February 2016 Accepted: 4 July 2016 Published: 18 July 2016
Abstract
Elusor macrurus is an endangered short-necked turtle restricted to the Mary River catchment in south-eastern Queensland. Shotgun sequencing of genomic DNA was used to generate a complete mitochondrial genome sequence for E. macrurus using the Illumina MiSeq platform. The mitogenome is 16 499 base pairs (bp) long with 37 genes arranged in the typical vertebrate order and a relatively short 918-bp control region, which does not feature extensive tandem repeats as observed in some turtles. Primers were designed to amplify a 1270-bp region that includes 81% of the typically hypervariable control region. Two haplotypes were detected in a sample of 22 wild-caught individuals from eight sites across its natural range. The Mary River turtle is a species with low mtDNA nucleotide variability relative to other Chelidae. The combination of a very restricted distribution and dramatic reduction in population size due to exploitation for the pet trade are the conditions likely to have led to very low mtDNA variability in this endangered species.
Additional keywords: control region, D loop, freshwater turtle, MiSeq, next generation sequencing.
References
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27, 573–580.| Tandem repeats finder: a program to analyze DNA sequences.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXhtVKmtrg%3D&md5=3c96e7cbaf41aab6caf3698f64e3c3ebCAS | 9862982PubMed |
Bernt, M., Donath, A., Juhling, F., Externbrink, F., Florentz, C., Fritzsch, G., Putz, J., Middendorf, M., and Stadler, P. F. (2013). MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69, 313–319.
| MITOS: improved de novo metazoan mitochondrial genome annotation.Crossref | GoogleScholarGoogle Scholar | 22982435PubMed |
Duchene, S., Frey, A., Alfaro-Nunez, A., Dutton, P. H., Gilbert, M. T. P., and Morin, P. A. (2012). Marine turtle mitogenome phylogenetics and evolution. Molecular Phylogenetics and Evolution 65, 241–250.
| Marine turtle mitogenome phylogenetics and evolution.Crossref | GoogleScholarGoogle Scholar | 22750111PubMed |
Faircloth, B. C., and Glenn, T. C. (2012). Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS One 7, e42543.
| Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xht1Olsb7K&md5=6b87ef2ee0e80dddd7918606189f2cd8CAS | 22900027PubMed |
Georges, A., and Thomson, S. (2006). Evolution and zoogeography of Australian freshwater turtles. In ‘Evolution and Zoogeography of Australasian Vertebrates’. (Eds J. R. Merrick, M. Archer, G. M. Hickey and M. S. Y. Lee.) pp. 291–308. (Auscipub Pty Ltd: Sydney.)
Georges, A., Birrell, J., Saint, K. M., McCord, W., and Donnellan, S. C. (1999). A phylogeny for side-necked turtles (Chelonia: Pleurodira) based on mitochondrial and nuclear gene sequence variation. Biological Journal of the Linnean Society 67, 213–246.
| A phylogeny for side-necked turtles (Chelonia: Pleurodira) based on mitochondrial and nuclear gene sequence variation.Crossref | GoogleScholarGoogle Scholar |
Georges, A., Spencer, R.-J., Welsh, M., Shaffer, H. B., Walsh, R., and Zhang, X. (2011). Application of the precautionary principle to taxa of uncertain status: the case of the Bellinger River turtle. Endangered Species Research 14, 127–134.
| Application of the precautionary principle to taxa of uncertain status: the case of the Bellinger River turtle.Crossref | GoogleScholarGoogle Scholar |
Georges, A., Zhang, X. W., Unmack, P., Reid, B. N., Le, M., and McCord, W. P. (2014). Contemporary genetic structure of an endemic freshwater turtle reflects Miocene orogenesis of New Guinea. Biological Journal of the Linnean Society 111, 192–208.
| Contemporary genetic structure of an endemic freshwater turtle reflects Miocene orogenesis of New Guinea.Crossref | GoogleScholarGoogle Scholar |
Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuboock, R., and Hofacker, I. L. (2008). The Vienna RNA Websuite. Nucleic Acids Research 36, W70–W74.
| The Vienna RNA Websuite.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXptlKkurg%3D&md5=f5f69cc0a0e6fd6dc570a7c9802a6673CAS | 18424795PubMed |
Hodges, K., Donnellan, S., and Georges, A. (2014). Phylogeography of the Australian freshwater turtle Chelodina expansa reveals complex relationships among inland and coastal bioregions. Biological Journal of the Linnean Society 111, 789–805.
| Phylogeography of the Australian freshwater turtle Chelodina expansa reveals complex relationships among inland and coastal bioregions.Crossref | GoogleScholarGoogle Scholar |
Hodges, K., Donnellan, S., and Georges, A. (2015). Significant genetic structure despite high vagility revealed through mitochondrial phylogeography of an Australian freshwater turtle (Chelodina longicollis). Marine and Freshwater Research 66, 1045–1056.
| Significant genetic structure despite high vagility revealed through mitochondrial phylogeography of an Australian freshwater turtle (Chelodina longicollis).Crossref | GoogleScholarGoogle Scholar |
Huey, J. A., Espinoza, T., and Hughes, J. M. (2013). Natural and anthropogenic drivers of genetic structure and low genetic variation in the endangered freshwater cod, Maccullochella mariensis. Conservation Genetics 14, 997–1008.
| Natural and anthropogenic drivers of genetic structure and low genetic variation in the endangered freshwater cod, Maccullochella mariensis.Crossref | GoogleScholarGoogle Scholar |
Hughes, J. M., Schmidt, D. J., Huey, J. A., Real, K. M., Espinoza, T., McDougall, A., Kind, P. K., Brooks, S., and Roberts, D. T. (2015). Extremely low microsatellite diversity but distinct population structure in a long-lived threatened species, the Australian lungfish Neoceratodus forsteri (Dipnoi). PLoS One 10, e0121858.
| Extremely low microsatellite diversity but distinct population structure in a long-lived threatened species, the Australian lungfish Neoceratodus forsteri (Dipnoi).Crossref | GoogleScholarGoogle Scholar | 25853492PubMed |
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P., and Drummond, A. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649.
| Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.Crossref | GoogleScholarGoogle Scholar | 22543367PubMed |
Le, M., Reid, B. N., McCord, W. P., Naro-Maciel, E., Raxworthy, C. J., Amato, G., and Georges, A. (2013). Resolving the phylogenetic history of the short-necked turtles, genera Elseya and Myuchelys (Testudines: Chelidae) from Australia and New Guinea. Molecular Phylogenetics and Evolution 68, 251–258.
| Resolving the phylogenetic history of the short-necked turtles, genera Elseya and Myuchelys (Testudines: Chelidae) from Australia and New Guinea.Crossref | GoogleScholarGoogle Scholar | 23563271PubMed |
Limpus, C. (2012). Freshwater turtles in the Mary River: review of biological data for turtles in the Mary River, with emphasis on Elusor macrurus and Elseya albagula. Queensland Government, Brisbane.
Magoc, T., and Salzberg, S. L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963.
| FLASH: fast length adjustment of short reads to improve genome assemblies.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtlGkur7M&md5=2c0d3d2c2c23dbf05f2c0bd505a3757cCAS | 21903629PubMed |
Micheli-Campbell, M. A., Campbell, H. A., Connell, M., Dwyer, R. G., and Franklin, C. E. (2013). Integrating telemetry with a predictive model to assess habitat preferences and juvenile survival in an endangered freshwater turtle. Freshwater Biology 58, 2253–2263.
| Integrating telemetry with a predictive model to assess habitat preferences and juvenile survival in an endangered freshwater turtle.Crossref | GoogleScholarGoogle Scholar |
Schmidt, D. J. (2015). The complete mitogenome of an Australian carp gudgeon, hybridogenetic biotype HAHB (Hypseleotris: Eleotridae). Mitochondrial DNA , .
| The complete mitogenome of an Australian carp gudgeon, hybridogenetic biotype HAHB (Hypseleotris: Eleotridae).Crossref | GoogleScholarGoogle Scholar | 26643618PubMed |
Seddon, J. M., Georges, A., Baverstock, P. R., and McCord, W. (1997). Phylogenetic relationships of chelid turtles (Pleurodira: Chelidae) based on mitochondrial 12S rRNA gene sequence variation. Molecular Phylogenetics and Evolution 7, 55–61.
| Phylogenetic relationships of chelid turtles (Pleurodira: Chelidae) based on mitochondrial 12S rRNA gene sequence variation.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2sXhtFGhu7g%3D&md5=90918230bbf3932f5c9898bfdaa65a21CAS | 9007020PubMed |
Souza, F. L., Cunha, A. F., Oliveira, M. A., Pereira, G. A. G., and Dos Reis, S. F. (2003). Preliminary phylogeographic analysis of the Neotropical freshwater turtle Hydromedusa maximiliani (Chelidae). Journal of Herpetology 37, 427–433.
| Preliminary phylogeographic analysis of the Neotropical freshwater turtle Hydromedusa maximiliani (Chelidae).Crossref | GoogleScholarGoogle Scholar |
Spinks, P. Q., Georges, A., and Shaffer, H. B. (2015). Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian short-necked turtles (Testudines: Chelidae). Copeia 103, 536–540.
| Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian short-necked turtles (Testudines: Chelidae).Crossref | GoogleScholarGoogle Scholar |
Todd, E. V., Blair, D., Farley, S., Farrington, L., Fitzsimmons, N. N., Georges, A., Limpus, C. J., and Jerry, D. R. (2013). Contemporary genetic structure reflects historical drainage isolation in an Australian snapping turtle, Elseya albagula. Zoological Journal of the Linnean Society 169, 200–214.
| Contemporary genetic structure reflects historical drainage isolation in an Australian snapping turtle, Elseya albagula.Crossref | GoogleScholarGoogle Scholar |
Todd, E. V., Blair, D., Georges, A., Lukoschek, V., and Jerry, D. R. (2014a). A biogeographical history and timeline for the evolution of Australian snapping turtles (Elseya: Chelidae) in Australia and New Guinea. Journal of Biogeography 41, 905–918.
| A biogeographical history and timeline for the evolution of Australian snapping turtles (Elseya: Chelidae) in Australia and New Guinea.Crossref | GoogleScholarGoogle Scholar |
Todd, E. V., Blair, D., and Jerry, D. R. (2014b). Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle, Emydura macquarii krefftii, from Australia. Ecology and Evolution 4, 606–622.
| Influence of drainage divides versus arid corridors on genetic structure and demography of a widespread freshwater turtle, Emydura macquarii krefftii, from Australia.Crossref | GoogleScholarGoogle Scholar | 25035802PubMed |
Wang, L., Zhou, X. M., Nie, L. W., Xia, X. Q., Liu, L., Jiang, Y., Huang, Z. F., and Jing, W. X. (2012). The complete mitochondrial genome sequences of Chelodina rugosa and Chelus fimbriata (Pleurodira: Chelidae): implications of a common absence of initiation sites (O–L) in pleurodiran turtles. Molecular Biology Reports 39, 2097–2107.
| The complete mitochondrial genome sequences of Chelodina rugosa and Chelus fimbriata (Pleurodira: Chelidae): implications of a common absence of initiation sites (O–L) in pleurodiran turtles.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhvVWmsLc%3D&md5=3272a76750b1063fcc7e496650b7eb75CAS | 21655955PubMed |
Wilson, A. C., Cann, R. L., Carr, S. M., George, M., Gyllensten, U. B., Helmbychowski, K. M., Higuchi, R. G., Palumbi, S. R., Prager, E. M., Sage, R. D., and Stoneking, M. (1985). Mitochondrial DNA and two perspectives on evolutionary genetics. Biological Journal of the Linnean Society 26, 375–400.
| Mitochondrial DNA and two perspectives on evolutionary genetics.Crossref | GoogleScholarGoogle Scholar |
Zhang, X. W., and Georges, A. (2014). A complete mitochondrial genome sequence for the Australian turtle, Chelodina longicollis, obtained using 454-pyrosequencing. Conservation Genetics Resources 6, 555–557.
| A complete mitochondrial genome sequence for the Australian turtle, Chelodina longicollis, obtained using 454-pyrosequencing.Crossref | GoogleScholarGoogle Scholar |
