Free Standard AU & NZ Shipping For All Book Orders Over $80!
Register      Login
Australian Journal of Zoology Australian Journal of Zoology Society
Evolutionary, molecular and comparative zoology
RESEARCH ARTICLE

The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)

Anna J. MacDonald A C , Theresa Knopp A , Mitzy Pepper B , J. Scott Keogh B and Stephen D. Sarre A
+ Author Affiliations
- Author Affiliations

A Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.

B Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.

C Corresponding author. Email: Anna.MacDonald@canberra.edu.au

Australian Journal of Zoology 63(2) 111-114 https://doi.org/10.1071/ZO14092
Submitted: 27 October 2014  Accepted: 7 April 2015   Published: 28 April 2015

Abstract

The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16 528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and the control region, conforming to the typical vertebrate gene order. The overall mitochondrial nucleotide composition is 31.7% A, 24.5% T, 30.5% C and 13.2% G. This corresponds to a total A+T content of 56.3%, which is similar to that of other squamate lizard genomes.


References

Alverson, A. J., Wei, X., Rice, D. W., Stern, D. B., Barry, K., and Palmer, J. D. (2010). Insights into the evolution of plant mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Molecular Biology and Evolution 27, 1436–1448.
Insights into the evolution of plant mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXmsVCqtbc%3D&md5=08ac46c1c816d75beace25154786bd3cCAS | 20118192PubMed |

Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, 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 |

Boore, J. L. (1999). Animal mitochondrial genomes. Nucleic Acids Research 27, 1767–1780.
Animal mitochondrial genomes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXivVersbo%3D&md5=d7c89332e25c51a156df47f64e3b8b89CAS | 10101183PubMed |

Donnellan, S. C., Hutchinson, M. N., and Saint, K. M. (1999). Molecular evidence for the phylogeny of Australian gekkonoid lizards. Biological Journal of the Linnean Society 67, 97–118.
Molecular evidence for the phylogeny of Australian gekkonoid lizards.Crossref | GoogleScholarGoogle Scholar |

Fujita, M. K., Boore, J. L., and Moritz, C. (2007). Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae). Molecular Biology and Evolution 24, 2775–2786.
Multiple origins and rapid evolution of duplicated mitochondrial genes in parthenogenetic geckos (Heteronotia binoei; Squamata, Gekkonidae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXnsVGhsw%3D%3D&md5=6f603be82eb54ff9d3714c23759b7a32CAS | 17921488PubMed |

Gardner, M. G., Fitch, A. J., Bertozzi, T., and Lowe, A. J. (2011). Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources 11, 1093–1101.
Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development.Crossref | GoogleScholarGoogle Scholar | 21679314PubMed |

Gissi, C, Iannelli, F, and Pesole, G (2008). Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 101, 301–320.
Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtFCrtb7K&md5=e3a3f82870a1cf4b0214ab622ea43f7aCAS | 18612321PubMed |

Jennings, W. B., Pianka, E. R., and Donnellan, S. (2003). Systematics of the lizard family Pygopodidae with implications for the diversification of Australian temperate biotas. Systematic Biology 52, 757–780.
Systematics of the lizard family Pygopodidae with implications for the diversification of Australian temperate biotas.Crossref | GoogleScholarGoogle Scholar | 14668116PubMed |

Kan, X.-Z., Yang, J.-K., Li, X.-F., Chen, L., Lei, Z.-P., Wang, M., Qian, C.-J., Gao, H., and Yang, Z.-Y. (2010). Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes. Genetics and Molecular Research 9, 1625–1633.
Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhtVKnsrvL&md5=3f20d307c41081602e65306d6c866d55CAS | 20730714PubMed |

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., Mentjies, 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 |

Kluge, A. G. (1976). Phylogenetic relationships in the lizard family Pygopodidae: an evaluation of theory, methods and data. Miscellaneous Publications, Museum of Zoology, University of Michigan 152, 1–7.

Kluge, A. G. (1987). Cladistic relationships in the Gekkonidae (Squamata, Sauria). Miscellaneous Publications, Museum of Zoology, University of Michigan 173, 1–54.

Kumazawa, Y., and Endo, H. (2004). Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Research 11, 115–125.
Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXkvVyhtbs%3D&md5=d2827dd0404ede5189e1472f2a194239CAS | 15449544PubMed |

Kumazawa, Y., Ota, H., Nishida, M., and Ozawa, T. (1996). Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Molecular Biology and Evolution 13, 1242–1254.
Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK28Xms1Siu7s%3D&md5=f6ff440b5558a17906fb2bdb63f8552cCAS | 8896377PubMed |

Kumazawa, Y., Ota, H., Nishida, M., and Ozawa, T. (1998). The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150, 313–329.
| 1:CAS:528:DyaK1cXmtFKgsL8%3D&md5=70414810b3eebede2ceeef1f03de76e9CAS | 9725849PubMed |

Lowe, T. M., and Eddy, S. R. (1997). tRNA-scan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25, 955–964.
tRNA-scan-SE: a program for improved detection of transfer RNA genes in genomic sequence.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2sXhvVahtrk%3D&md5=b7a4343021f43cbfbd42b4f242454c81CAS | 9023104PubMed |

Macey, J. R., Papenfuss, T. J., Kuehl, J. V., Fourcade, H. M., and Boore, J. L. (2004). Phylogenetic relationships among Amphisbaenian reptiles based on complete mitochondrial genomic sequences. Molecular Phylogenetics and Evolution 33, 22–31.
Phylogenetic relationships among Amphisbaenian reptiles based on complete mitochondrial genomic sequences.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXmvFCrsLk%3D&md5=6b4e1ead5468059c593fa111910afae3CAS | 15324836PubMed |

Macey, J. R., Fong, J. J., Kuehl, J. V., Shafiei, S., Ananjeva, N. B., Papenfuss, T. J., and Boore, J. L. (2005). The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Molecular Phylogenetics and Evolution 36, 188–193.
The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXkt1Oiu74%3D&md5=8abc753a186b50aad7e997e7d310373bCAS | 15904865PubMed |

Meglécz, E., Nève, G., Biffin, E., and Gardner, M. G. (2012). Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species. PLoS One 7, e40861.
Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species.Crossref | GoogleScholarGoogle Scholar | 22815847PubMed |

Moritz, C. (1991). The origin and evolution of parthenogenesis in Heteronotia binoei (Gekkonidae): evidence for recent and localized origins of widespread clones. Genetics 129, 211–219.
| 1:STN:280:DyaK38%2FjvV2ntg%3D%3D&md5=6891becc0dd451f5cb658966f4860b56CAS | 1682211PubMed |

Mulcahy, D. G., Noonan, B. P., Moss, T., Townsend, T. M., Reeder, T. W., Sites, J. W., and Wiens, J. J. (2012). Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles. Molecular Phylogenetics and Evolution 65, 974–991.
Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles.Crossref | GoogleScholarGoogle Scholar | 22982760PubMed |

Okajima, Y., and Kumazawa, Y. (2010). Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications. BMC Evolutionary Biology 10, 141.
Mitochondrial genomes of acrodont lizards: timing of gene rearrangements and phylogenetic and biogeographic implications.Crossref | GoogleScholarGoogle Scholar | 20465814PubMed |

Pyron, R. A., Burbrink, F. T., and Wiens, J. J. (2013). A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology 13, 93.
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes.Crossref | GoogleScholarGoogle Scholar | 23627680PubMed |

Seutin, G., Lang, B. F., Mindell, D. P., and Morais, R. (1994). Evolution of the WANCY region in amniote mitochondrial DNA. Molecular Biology and Evolution 11, 329–334.
| 1:CAS:528:DyaK2cXlt1Knt70%3D&md5=5a2aacc48f31de53f61c4286d789fb31CAS | 8015429PubMed |

Wiens, J. J., Hutter, C. R., Mulcahy, D. G., Noonan, B. P., Townsend, T. M., Sites, J. W., and Reeder, T. W. (2012). Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters 8, 1043–1046.
Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species.Crossref | GoogleScholarGoogle Scholar | 22993238PubMed |

Zevering, C. E., Moritz, C., Heideman, A., and Sturm, R. A. (1991). Parallel origins of duplications and the formation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae). Journal of Molecular Evolution 33, 431–441.
Parallel origins of duplications and the formation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK38Xlt1Kkuw%3D%3D&md5=8661e2d65c8bb201517928a5a7074b68CAS | 1960740PubMed |

Zhang, P., Liang, D., Mao, R.-L., Hillis, D. M., Wake, D. B., and Cannatella, D. C. (2013). Efficient sequencing of Anuran mtDNAs and a mitogenomic exploration of the phylogeny and evolution of frogs. Molecular Biology and Evolution 30, 1899–1915.
Efficient sequencing of Anuran mtDNAs and a mitogenomic exploration of the phylogeny and evolution of frogs.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhtFSrt73M&md5=94a0742f9943a84f985c717bc61b1025CAS | 23666244PubMed |

Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. (2000). A greedy algorithm for aligning DNA sequences. Journal of Computational Biology 7, 203–214.
A greedy algorithm for aligning DNA sequences.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXktl2qsrY%3D&md5=a677a619b8219877fd6e487b0e86d2ecCAS | 10890397PubMed |

Zhou, K., Li, H., Han, D., Bauer, A. M., and Feng, J. (2006). The complete mitochondrial genome of Gekko gecko (Reptilia: Gekkonidae) and support for the monophyly of Sauria including Amphisbaenia. Molecular Phylogenetics and Evolution 40, 887–892.
The complete mitochondrial genome of Gekko gecko (Reptilia: Gekkonidae) and support for the monophyly of Sauria including Amphisbaenia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XotFWkurw%3D&md5=f10b75f104e8e29e7e85473e5cd8b922CAS | 16750399PubMed |