Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa)

Zoological Studies

Volumn 50, Issue 4, 2011, Pages 513-524

  Lin, Mei Fang ^a,d   Luzon, Katrina S ^b   Licuanan, Wilfredo Y ^c   Ablan Lagman, Maria Carmen ^c   Chen, Chaolun A ^a,d,e,f  

^a BIODIVERSITY RESEARCH CENTER   (Taiwan)

^b University of the Philippines Diliman   (Philippines)

^c DE LA SALLE UNIVERSITY   (Philippines)

^d NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^e NATIONAL TAITUNG UNIVERSITY   (Taiwan)

^f JAMES COOK UNIVERSITY   (Australia)

Author keywords

Mitochondrial genomes; Phylogeny; Scleractinian corals; Universal primers

Indexed keywords

ANTHOZOA; CNIDARIA; EUPHYLLIA; EUPHYLLIA ANCORA; FUNGIACYATHUS STEPHANUS; GALAXEA FASCICULARIS; GONIOPORA COLUMNA; OULASTREA CRISPATA; PAVONA VENOSA; POLYCYATHUS; PORITES OKINAWENSIS; SCLERACTINIA; TUBASTRAEA COCCINEA;

EID: 79959919327     PISSN: 10215506     EISSN: 1810522X     Source Type: Journal    
DOI: None     Document Type: Article

References (45)

1. Akaike H. 1974. New look at statistical-model identification. IEEE T. Automat. Contr. 19: 716-723.
2. Boore JL. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27: 1767-1780.
3. Budd AF, SL Romano, ND Smith, MS Barbeitos. 2010. Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data. Integr. Comp. Biol. DOI: 10.1093/icb/icq062.
4. Cairns SD. 1999. Species richness of recent Scleractinia. Atoll Res. Bull. (National Museum of Natural History Smithsonian Institution Washington, DC, USA) 459: 1-46.
5. Chen C, CY Chiou, CF Dai, CA Chen. 2008a. Unique mitogenomic features in the scleractinian family Pocilloporidae (Scleractinia: Astrocoeniina). Mar. Biotech. 10: 538-553.
6. Chen C, CF Dai, S Plathong, CY Chiou, CA Chen. 2008b. 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. Mol. Phylogenet. Evol. 46: 19-33.
7. Chen CA, CC Wallace, J Wolstenholme. 2002. Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals. Mol. Phylogenet. Evol. 23: 137-149.
8. Chen CA, JK Yu. 2000. Universal primers for amplification of mitochondrial small subunit ribosomal RNA-encoding gene in scleractinian corals. Mar. Biotech. 2: 146-153.
9. Chen IP, CY Tang, CY Chiou, JH Hsu, NV Wei, CC Wallace et al. 2008. Comparative analysis of coding and noncoding DNA regions indicate that Acropora (Anthozoa: Scleractina) possesses a similar evolutionary tempo of nuclear vs. mitochondrial genomes as in plants. Mar. Biotech. DOI: 10.1007/s10126-008-9129-2.
10. Chen IP, CY Tang, CY Chiou, JH Hsu, NV Wei, CC Wallace et al. 2009. Comparative analysis of coding and noncoding DNA regions indicate that Acropora (Anthozoa: Scleractina) possesses a similar evolutionary tempo of nuclear vs. mitochondrial genomes as in plants. Mar. Biotech. DOI: 10.1007/s10126-008-9129-2.
11. Coates AG, JBC Jackson, LS Collins, TM Cronin, HJ Dowsett, LM Bybell et al. 1992. Closure of the Isthmus of Panama: the near-shore marine record of Costa Rica and western Panama. Geol. Soc. Am. Bull. 104: 814-828.
12. Dai CF, S Horng. 2009a. Scleractinia fauna of Taiwan I. Taipei, Taiwan: National Taiwan Univ.
13. Dai CF, S Horng. 2009b. Scleractinia fauna of Taiwan II. Taipei, Taiwan: National Taiwan Univ.
14. Fautin DG, JM Lowenstein. 1992. Phylogenetic relationships among scleractinians, actiniarians, and corallimorpharians (Coelenterata: Anthozoa). Proc. Seventh Int. Coral Reef Symp. 2: 665-670.
15. Fukami H, CA Chen, AF Budd, A Collins, C Wallace, YY Chuang et al. 2008. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (order Scleractinia, class Anthozoa, phylum Cnidaria). PLoS ONE 3: e3222.
16. Fukami H, CA Chen, CY Chiou, N Knowlton. 2007. Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of scleractinian corals. J. Mol. Evol. 64: 591-600
17. Fukami H, N Knowlton. 2005. Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia). Coral Reefs 24: 410-417.
18. Gish W, DJ States. 1993. Identification of protein coding regions by database similarity search. Nat. Genet. 3: 266-272.
19. Hellberg ME. 2006. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol. Biol. 6: 24. DOI: 10.1186/1471-2148-6-24.
20. Kalendar R. 2008. FastPCR: a PCR primer and probe design and repeat sequence searching software with additional tools for the manipulation and analysis of DNA and protein. Available at http://www.biocenter.helsinki.fi/bi/ programs/fastpcr.htm n.d. web. 24 Oct. 2006.
21. Kitahara MV, SD Cairns, J Stolarski, D Blair, DJ Miller. 2010a. A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial COI sequence data. PLoS ONE 5: e11490. DOI: 10.1371/ journal.pone.0011490
22. Kitahara MV, SD Vairns, DJ Miller. 2010b. Monophyletic origin of Caryophyllia (Scleractinia, Caryophylliidae), with description of six new species. Syst. Biodivers. 8: 91-118.
23. Lowe TM, SR Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
24. Medina M, AG Collins, TL Takaoka, JV Kuehl, JL Boore. 2006. Naked corals: skeleton loss in Scleractinia. Proc. Natl. Acad. Sci. USA 103: 9096-9100.
25. Miya M, M Nishida. 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Mar. Biotech. 1: 416-426.
26. Nylander JAA. 2004. MrModeltest v2. Program distributed by the author. Uppsala, Sweden: Evolutionary Biology Centre, Uppsala Univ.
27. Romano SL, SD Cairns. 2000. Molecular phylogenetic hypotheses for the evolution of scleractinian corals. B. Mar. Sci. 67: 1043-1068.
28. Romano SL, SR Palumbi. 1996. Evolution of scleractinian corals inferred from molecular systematics. Science 271: 640-642.
29. Romano SL, SR Palumbi. 1997. Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals. J. Mol. Evol. 45: 397-411.
30. Ronquist F, JP Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
31. Sanger F, S Nicklen, AR Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74: 5463-5467.
32. Selosse M, B Albert, B Godelle. 2001. Reducing the genome size of organelles favours gene transfer to the nucleus. Trends Ecol. Evol. 16: 135-141.
33. Shearer TL, MJH van Oppen, SL Romano, G Wörheide. 2002. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol. Ecol. 11: 2475-2487.
34. Simon C, TR Buckley, F Frati, JB Stewart, AT Beckenbach. 2006. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu. Rev. Ecol. Syst. 37: 545-579.
35. Sorenson MD, JC Ast, DE Dimcheff, T Yuri, DP Mindell. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Mol. Phylogenet. Evol. 12: 105-114.
36. Stefani F, F Benzoni, M Pichon, G Mitta, P Galli. 2008. Genetic and morphometric evidence for unresolved species boundaries in the coral genus Psammocora (Cnidaria; Scleractinia). Hydrobiologia. DOI: 10.1007/s10750-007-9092-3.
37. Takabayashi M, DA Carter, JV Lopez, O Hoegh-Guldberg. 2003. Genetic variation of the scleractinian coral Stylophora pistillata, from western Pacific reefs. Coral Reefs 22: 17-22.
38. Tamura K, J Dudley, M Nei, S Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software vers. 4.0. Mol. Biol. Evol. 24: 1596-1599.
39. Thompson JD, DG Higgins, TJ Gibson. 1994. ClustalW improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
40. Tseng CC, CC Wallace, CA Chen. 2005. Mitogenomic analysis of Montipora cactus and Anacropora matthai (Cnidaria; Scleractinia; Acroporidae) indicates an unequal rate of mitochondrial evolution among Acroporidae corals. Coral Reefs 24: 502-508.
41. van Oppen MJH, J Catmull, BJ McDonald, NR Hislop, PJ Hagerman, DJ Miller. 2002. The mitochondrial genome of Acropora tenuis (Cnidaria: Scleractinia) contains a large group I intron and a candidate control region. J. Mol. Evol. 55: 1-13.
42. van Oppen MJH, NR Hislop, PJ Hagerman, DJ Miller. 1999b. Gene content and organization in a segment of the mitochondrial genome of the scleractinian coral Acropora tenuis: major differences in gene order within the anthozoan subclass Zoantharia. Mol. Biol. Evol. 16: 1812-1815.
43. van Oppen MJH, BL Willis, DJ Miller. 1999a. Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora. P. Roy. Soc. B Biol. Sci. 266: 179-183.
44. Veron JEN. 2000. Corals of the world, Vol. 2. Queensland, Australia: Australian Institute of Marine Science and CRR, pp. 66-81.
45. Veron JEN. 2008. A reef in time: the Great Barrier Reef from beginning to end. Cambridge, MA, USA: Belknap Press of Harvard Univ. Press.