The complete mitochondrial genomes of needle corals, Seriatopora spp. (Scleractinia: Pocilloporidae): An idiosyncratic atp8, duplicated trnW gene, and hypervariable regions used to determine species phylogenies and recently diverged populations

Molecular Phylogenetics and Evolution

Volumn 46, Issue 1, 2008, Pages 19-33

  Chen, Chienhsun ^a,b   Dai, Chang Feng ^a   Plathong, Sakanan ^c   Chiou, Chih Yung ^b   Chen, Chaolun Allen ^a,b  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b BIODIVERSITY RESEARCH CENTER   (Taiwan)

^c PRINCE OF SONGKLA UNIVERSITY   (Thailand)

Author keywords

Complete mitochondrial genomes; Control region; Idiosyncratic ATP8; Scleractinia; Seriatopora; tRNA duplication

Indexed keywords

MITOCHONDRIAL DNA; TRANSFER RNA; TRYPTOPHAN TRANSFER RNA;

AMINO ACID SEQUENCE; ANIMAL; ANTHOZOA; ARTICLE; CHEMISTRY; CLASSIFICATION; CODON; DUPLICATE GENE; GENETIC VARIABILITY; GENETICS; GENOME; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

AMINO ACID SEQUENCE; ANIMALS; ANTHOZOA; BASE SEQUENCE; CODON; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, DUPLICATE; GENES, MITOCHONDRIAL; GENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, TRANSFER; RNA, TRANSFER, TRP; VARIATION (GENETICS);

ANTHOZOA; POCILLOPORIDAE; SCLERACTINIA; SERIATOPORA; SERIATOPORA CALIENDRUM; SERIATOPORA HYSTRIX;

EID: 37249037188     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.09.013     Document Type: Article

References (68)

1. Beagley C.T., Okimoto R., and Wolstenholme D.R. The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, a near-standard genetic code. Genetics 148 (1998) 1091-1108
2. Ser (UCN) gene. Genetics 152 (1999) 573-652
3. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27 (1999) 573-580
4. Benzie J.A.H. Genetic structure of marine organisms and SE Asian biogeography. In: Hall R., and Holloway J.D. (Eds). Biogeography and Geological Evolution of SE Asia (1998), Backhuys Publishers, The Netherlands 197-209
5. Benzie J.A.H. Genetic structure of coral reef organisms: ghosts of dispersal past. American Zoologist 39 (1999) 131-145
6. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Research 27 (1999) 1767-1780
7. Burger G., Gray M.W., and Lang B.F. Mitochondrial genomes: anything goes. Trends in Ecology and Evolution 19 (2003) 709-716
8. Chen, C., Dai, C.-F., Fukami, H., Knowlton, N., Chen, C.A., 2006. Evolutionary mitogenomics of pocilloporid corals: ATP8 gene loss, a novel open reading frame (ORF) and phylogenetic utility. First Asia Pacific Coral Reef Symposium, Hong Kong, M39.
9. Chen C.A., Wallace C.C., and Wolstenholme J. Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals. Molecular Phylogenetics and Evolution 23 (2002) 137-149
10. Chen C.A., and Yu J.-K. Universal primers for amplification of mitochondrial small subunit ribosomal RNA-encoding gene in scleractinian corals. Marine Biotechnology 2 (2000) 146-153
11. Cheng S., Chang S.Y., Gravitt P., and Respess R. Long PCR. Nature 369 (1994) 684-685
12. Chern C.-S., and Wang J. Numerical study of the upper-layer circulation in the South China Sea. Journal of Oceanography 59 (2003) 11-24
13. Chu P.C., and Guihua W. Seasonal variability of the thermohaline front in the central South China Sea. Journal of Oceanography 59 (2003) 65-78
14. Chuang, Y.-Y., 2006. Mitogenomics and molecular evolution of the group I intron in the cytochrome oxidase I gene of Siderastrea (Cnidaria;Scleractinia;Siderastreidae). Master's thesis. Institute of Oceanography. National Taiwan University, Taipei, Taiwan.
15. Dellaporta S.L., Xu A., Sagasser S., Jakob W., Moreno M.A., Buss L.W., and Schierwater B. Mitochondrial genome of Trichoplax adhaerens supports Placozoa as the basal lower metazoan phylum. Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 8751-8756
16. Devenish R.J., Papakonstantinou T., Galanis M., Law R.H., Linnane A.W., and Nagley P. Structure/function analysis of yeast mitochondrial ATP synthase subunit 8. Annals of the New York Academy of Sciences 671 (1992) 403-414
17. Di Giulio M. On the origin of the transfer RNA molecule. Journal of Theoretical Biology 159 (1992) 199-214
18. Di Giulio M. The origin of the tRNA molecule: implications for the origin of protein synthesis. Journal of Theoretical Biology 226 (2004) 89-93
19. Domart-Coulon I., Tambutté S., Tambutté E., and Allemand D. Short term viability of soft tissue detached from the skeleton of reef-building corals. Journal of Experimental Marine Biology and Ecology 309 (2004) 199-217
20. Domart-Coulon I.J., Elbert D.C., Scully E.P., Calimlim P.S., and Ostrander G.K. Aragonite crystallization in primary cell cultures of multicellular isolates from a hard coral, Pocillopora damicornis. Proceedings of the National Academy of Sciences of the United States of America 98 (2001) 11885-11890
21. Frost S.H. Oligocene reef coral biogeography, Caribbean and western Tethys. Bureau de Recherches Géologiques et Minières (France) 89 (1977) 342-352
22. Fukami H., Chen C.A., Chiou C.-Y., and Knowlton N. Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of scleractinian corals. Journal of Molecular Evolution 64 (2007) 591-600
23. Fukami, H., Chen, C.A., Knowlton, N., 2006. Chaos of the scleractinian coral family. First Asia Pacific Coral Reef Symposium. Hong Kong, pp M40.
24. Fukami H., and Knowlton N. Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia). Coral Reefs 24 (2005) 410-417
25. Gish W., and States D.J. Identification of protein coding regions by database similarity search. Nature Genetics 3 (1993) 266-272
26. Gissi C., Iannelli F., and Pesole G. Complete mtDNA of Ciona intestinalis reveals extensive gene rearrangement and the presence of an atp8 and an extra trnM gene in ascidians. Journal of Molecular Biology 58 (2004) 376-389
27. Goddard, M.R., Leigh, J., Roger, A.J., Pemberton, A.J., 2006. Invasion and persistence of a selfish gene in the Cnidaria. PLoS ONE 1, e3. doi: 10.1371/journal.pone.0000003.
28. Gonnet G.H., Cohen M.A., and Benner S.A. Exhaustive matching of the entire protein sequence database. Science 256 (1992) 1443-1445
29. Gregory J.W., and Trench J.B. Eocene corals from the Fly River, New Guinea. Geological Magazine 6 481-488 (1916) 529-536
30. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41 (1999) 95-98
31. He Y., Jones J., Armstrong M., Lamberti F., and Moens M. The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): considerable economization in the length and structural features of encoded genes. Journal of Molecular Biology 61 (2005) 819-883
32. Hellberg M.E. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evolutionary Biology 6 (2006) 24 doi:10.1186/1471-2148-1186-1124
33. Hoffmann R.J., Boore J.L., and Brown W.M. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131 (1992) 397-412
34. Hu M., Chilton N.B., and Gasser R.B. The mitochondrial genome of Strongyloides stercoralis (Nematoda)-idiosyncratic gene order and evolutionary implications. International Journal for Parasitology 33 (2003) 1393-1408
35. Huelsenbeck J.P., and Ronquist F.R. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
36. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16 (1980) 111-120
37. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5 (2004) 150-163
38. Kyte J., and Doolittle R.F. A simple method for displaying the hydrophobic character of a protein. Journal of Molecular Biology 157 (1982) 105-142
39. Lavrov D.V., and Brown W.M. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics 157 (2001) 621-637
40. Le T.H., Blair D., Agatsuma T., Humair P.-F., Campbell N.J.H., Iwagami M., Littlewood D.T.J., Peacock B., Johnson D.A., Bartley J., Rollinson D., Herniou E.A., Zarlenga D.S., and McManus D.P. Phylogenies inferred from mitochondrial gene orders - a cautionary tale from the parasitic flatworms. Molecular Biology and Evolution 17 (2000) 1123-1125
41. Lowe T.M., and Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25 (1997) 955-964
42. Medina M., Collins A.G., Takaoka T.L., Kuehl J.V., and Boore J.L. Naked corals: Skeleton loss in scleractinia. Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 9096-9100
43. Medina M., Weil E., and Szmant A.M. Examination of the Montastraea annularis species complex (Cnidaria : Scleractinia) using ITS and COI sequences. Marine Biotechnology 1 (1999) 89-97
44. Morton B., and Blackmore G. South China Sea. Marine Pollution Bulletin 42 (2001) 1236-1263
45. Nei M., and Kumar S. Molecular Evolution and Phylogenetics (2000), Oxford University Press, Oxford
46. Pandolfi J.M., Lovelock C.E., and Budd A.F. Character release following extinction in a Caribbean reef coral species complex. Evolution 56 (2002) 479-501
47. Papakonstantinou T., Galanis M., Nagley P., and Devenish R.J. Each of three positively-charged amino acids in the C-terminal region of yeast mitochondrial ATP synthase subunit 8 is required for assembly. Biochimica et Biophysica Acta 1144 (1993) 22-32
48. Papakonstantinou T., Law R.H., Nagley P., and Devenish R.J. Non-functional variants of yeast mitochondrial ATP synthase subunit 8 that assemble into the complex. Biochemistry and Molecular Biology International 39 (1996) 253-260
49. Papakonstantinou T., Law R.H.P., Nesbitt W.S., Nagley P., and Devenish R.J. Molecular genetic analysis of the central hydrophobic domain of subunit 8 of yeast mitochondrial ATP synthase. Current Genetics 30 (1996) 12-18
50. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
51. Romano S.L., and Palumbi S.R. Evolution of scleractinian corals inferred from molecular systematics. Science 271 (1996) 640-642
52. Romano S.L., and Palumbi S.R. Molecular evolution of a portion of the mitochondrial 16 S ribosomal gene region in scleractinian corals. Journal of Molecular Evolution 45 (1997) 397-411
53. Sambrook J., and Rusell D.W. Molecular Cloning: A Laboratory Manual (2001), Cold Spring Harbor Laboratory Press, New York
54. Shearer T.L., van Oppen M.J.H., Romano S.L., and Worheide G. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Molecular Ecology 11 (2002) 2475-2487
55. Snell T.L. Low levels of mitochondrial sequence variation in scleractinian corals. In: Hopley D., Hopley P., Tamelander J., and Done T. (Eds). Ninth International Coral Reef Symposium (2000), Smithsonian Tropical Research Institute, Bali, Indonesia 21
56. Snell T.L., Sammarco P.W., and Foltz D.W. Variation in morphology vs conservation of a mitochondrial gene in Montastraea cavernosa (Cnidaria, Scleractinia). Gulf of Mexico Science 16 (1998) 188-195
57. Swofford D.L. PAUP: phylogenetic analysis using parsimony (and other methods) (1999), Sinauer Associates, Sunderland, MA
58. Thompson J.D., Higgins D.G., and Gibson T.J. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22 (1994) 4673-4680
59. Tseng C.-C., Wallace C.C., and Chen C.A. Mitogenomic analysis of Montipora cactus and Anacropora matthai (cnidaria; scleractinia; acroporidae) indicates an unequal rate of mitochondrial evolution among Acroporidae corals. Coral Reefs 2005 (2005) 502-508
60. van Oppen M.J.H., Catmull J., McDonald B.J., Hislop N.R., Hagerman P.J., and Miller D.J. The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group 1 intron and a candidate control region. Journal of Molecular Evolution 55 (2002) 1-13
61. van Oppen M.J.H., Willis B.L., and Miller D.J. Atypical low rate of cytochrome b evolution in the scleractinian coral genus Acropora. Proceedings of the Royal Society B: Biological Sciences 266 (1999) 179-183
62. Varkey M.J., Murty V.S.N., and Suryanarayana A. Physical oceanography of the Bay of Bengal and Andaman Sea. Oceanography and Marine Biology 34 (1996) 1-70
63. Veron J.E.N. Corals of the world (2000), Australian Institute of Marine Science, Queensland, Australia
64. Veron J.E.N., and Pichon M. Scleractinia of Eastern Australia. Part I. Thamnasteriidae, Astrocoeniidae and Pocilloporidae. Australian Institute of Marine Science Monograph Series 1 (1976) 1-86
65. Watanabe T., Nishida M., Watanabe K., Wewengkang D.S., and Hidaka M. Polymorphism in nucleotide sequence of mitochondrial intergenic region in scleractinian coral (Galaxea fascicularis). Marine Biotechnology 7 (2005) 33-39
66. Wolstenholme D.R. Animal mitochondrial DNA: Structure and evolution. International Review of Cytology 141 (1992) 173-216
67. Yokobori S.-i., Ueda T., Feldmaier-Fuchs G., Pääbo S., Ueshima R., Kondow A., Nishikawa K., and Watanabe K. Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics 153 (1999) 1851-1862
68. Zuker M. Calculating nucleic acid secondary structure. Current Opinion in Structural Biology 10 (2000) 303-310