Evolution of gastropod mitochondrial genome arrangements

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  Grande, Cristina ^a,b   Templado, José ^a   Zardoya, Rafael ^a  

^a MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASCOBULLA FRAGILIS; GASTROPOD; GENE REARRANGEMENT; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; MOLLUSC; MYOSOTELLA MYOSOTIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ONCHIDELLA CELTICA; PYRAMIDELLA DOLABRATA; SIPHONARIA PECTINATA; ANIMAL; CLASSIFICATION; DNA SEQUENCE; GENETICS; MITOCHONDRIAL GENOME; PHYLOGENY; POLYMERASE CHAIN REACTION;

APOGASTROPODA; ASCOBULLA FRAGILIS; CAENOGASTROPODA; DOCOGLOSSA; EUTHYNEURA (GASTROPODS); GASTROPODA; HETEROBRANCHIA; METAZOA; MYOSOTELLA MYOSOTIS; ONCHIDELLA CELTICA; OPISTHOBRANCHIA; PULMONATA; PYRAMIDELLA DOLABRATA; SIPHONARIA PECTINATA; VERTEBRATA; VETIGASTROPODA;

ANIMALS; EVOLUTION, MOLECULAR; GASTROPODA; GENE REARRANGEMENT; GENOME, MITOCHONDRIAL; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 41849149995     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-61     Document Type: Article

References (94)

1. Animal mitochondrial genome: structure and evolution. DR Wolstenholme, Int Rev Cytol 1992 141 172 216
2. Sequencing and comparing whole mitochondrial genomes of animals. JL Boore JR Macey M Medina, Methods Enzymol 2005 395 311 348 15865975
3. Eukaryotae Organelles Taxonomy List. http://www.ncbi.nlm.nih.gov/genomes/ genlist.cgi?taxid=2759&type=4&name=Eukaryotae%20Organelles
4. Sequence and gene organization of the chicken mitochondrial genome - a novel gene order in higher vertebrates. P Desjardins R Morais, J Mol Biol 1990 212 599 634 10.1016/0022-2836(90)90225-B 2329578
5. A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. D San Mauro DJ Gower R Zardoya M Wilkinson, Mol Biol Evol 2006 23 227 234 10.1093/molbev/msj025 16177229
6. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. JL Boore WM Brown, Curr Opin Genet Dev 1998 8 668 674 10.1016/S0959-437X(98)80035-X 9914213
7. Rare genomic changes as a tool for phylogenetics. A Rokas PWH Holland, TREE 2000 15 454 459 11050348
8. High-performance algorithm engineering for computational phylogenetics. BME Moret DA Bader T Warnow, J Supercomput 2002 22 99 110 10.1023/A: 1014362705613
9. A Bayesian approach to the estimation of ancestral genome arrangements. B Larget JB Kadane DL Simon, Mol Phylogenet Evol 2005 36 214 223 10.1016/j.ympev.2005.03.026 15893477
10. A Bayesian analysis of metazoan mitochondrial genome arrangements. B Larget DL Simon JB Kadane D Sweet, Mol Biol Evol 2005 22 486 495 10.1093/molbev/msi032 15525697
11. Complete sequence of the mitochondrial DNA of the primitive opisthobranch gastropod Pupa strigosa: systematics implication of the genome organization. A Kurabayashi R Ueshima, Mol Biol Evol 2000 17 266 277 10677849
12. Complete sequence and gene organization of the mitochondrial genome of the land snail Albinaria coerulea. E Hatzoglou GC Rodakis R Lecanidou, Genetics 1995 140 1353 1366 7498775
13. Complete DNA Sequence of the mitochondrial genome of Cepaea nemoralis (Gastropoda: Pulmonata). JA Terrett S Miles RH Thomas, J Mol Evol 1996 42 160 168 10.1007/BF02198842 8919868
14. The complete mitochondrial genome of the nudibranch Roboastra europaea (Mollusca: Gastropoda) supports the monophyly of opisthobranchs. C Grande J Templado JL Cervera R Zardoya, Mol Biol Evol 2002 19 1672 1685 12270894
15. The mitochondrial genome of Biomphalaria glabrata (Gastropoda: Basommatophora), intermediate host of Schistosoma mansoni. RJ DeJong AM Emery CM Adema, J Parasitol 2004 90 991 997 10.1645/GE-284R 15562597
16. Mitochondrial DNA sequence and gene organization in Australian backup abalone Haliotis rubra (leach). BT Maynard LJ Kerr JM McKiernan ES Jansen PJ Hanna, Mar Biotechnol (NY) 2005 7 645 658 10.1007/s10126-005-0013-z 16206015
17. Complete DNA sequence of the mitochondrial genome of the sea-slug, Aplysia californica: conservation of the gene order in Euthyneura. B Knudsen AB Kohn B Nahir CS McFadden LL Moroz, Mol Phylogenet Evol 2006 38 459 469 10.1016/j.ympev.2005.08.017 16230032
18. Rolling circle amplification of metazoan mitochondrial genomes. WB Simison DR Lindberg JL Boore, Mol Phylogenet Evol 2006 39 562 567 10.1016/j.ympev.2005.11.006 16360323
19. Complete mitochondrial DNA sequence of a Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis: Gene order and gastropod phylogeny. PK Bandyopadhyay BJ Stevenson MT Cady BM Olivera DR Wolstenholme, Toxicon 2006 48 29 43 10.1016/j.toxicon.2006.04.013 16806344
20. Evolution of pulmonate gastropod mitochondrial genomes: Comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. N Yamazaki R Ueshima JA Terret S Yokobori M Kaifu R Segawa T Kobayashi K Numachi T Ueda K Nishikawa K Watanabe RH Thomas, Genetics 1997 145 749 758 9055084
21. Partial sequence of the mitochondrial genome of Littorina saxatilis: relevance to gastropod phylogenetics. CS Wilding PJ Mill J Grahame, J Mol Evol 1999 48 348 359 10.1007/PL00006479 10093225
22. Partial mitochondrial genome organization of the heterostrophan gastropod Omalogyra atomus and its systematic significance. A Kurabayashi R Ueshima, Venus 2000 59 7 18
23. J Thiele, Handbuch der Systematischen Weichtierkunde, Jena 1931 1
24. Die Geruchsorgane und das Nervensystem der Mollusken. Zeitschrift für Wissenschaftliche Zoologie. J Spengel, Leipzig 1881 35 333 383
25. Systematics of prosobranch gastropods. AN Golikov YI Starobogatov, Malacologia 1975 15 185 232
26. On the origin and evolution of major gastropods group, with special reference to the streptoneura. G Haszprunar, J Moll Stud 1988 54 367 441 10.1093/mollus/54.4.367
27. Synapomorphies and plesiomorphies in higher calssification of Mollusca. L Salvini-Plawen G Steiner, Origin and evolutionary radiation of the Mollusca London, The Malacological Society of London, Taylor J, 1996 29 51
28. Towards a phylogeny of gastropod molluscs: Analysis using morphological characters. WF Ponder DR Lindberg, Zool J Linn Soc 1997 119 83 265 10.1006/zjls.1996.0066
29. Details of gastropod phylogeny inferred from 18s rRNA sequences. B Winnepenninckx G Steiner T Backeljau R de Wachter, Mol Phylogenet Evol 1998 9 55 63 10.1006/mpev.1997.0439 9479694
30. Gastropod evolutionary rates and phylogenetic relationships assessed using partial 28S rDNA and histone H3 sequences. DJ Colgan WF Ponder PE Eggler, Zoologica Scripta 2000 29 29 63 10.1046/j.1463-6409.2000.00021.x
31. A molecular phylogeny of the Patellogatropoda (Mollusca: Gastropoda). MG Harasewych AG McArthur, Mar Biol 2000 137 183 194 10.1007/s002270000332
32. Phylogeny of some gastropod mollusks derived from 18s rRNA sequences with emphasis on the Euthyneura. SH Yoon W Kim, The Nautilus 2000 114 84 92
33. Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca). DJ Colgan WF Ponder E Beacham JM Macaranas, Mol Phylogenet Evol 2006 17127080
34. Gastropod phylogeny based on six segments from four genes representing coding or non-coding and mitochondrial or nuclear DNA. DJ Colgan WF Ponder E Beacham JM Macaranas, Molluscan Research 2003 23 123 148 10.1071/MR03002
35. The Vetigastropoda and the systematics of streptoneurous gastropods (Mollusca). L Salvini-Plawen G Haszprunar, J Zool London A 1987 211 747 770
36. Gastropod phylogeny and systematics. R Bieler, Annu Rev Ecol Syst 1992 23 311 338 10.1146/annurev.es.23.110192.001523
37. Molecular phylogeny of Euthyneura (Mollusca: Gastropoda). C Grande J Templado JL Cervera R Zardoya, Mol Biol Evol 2004 21 303 313 10.1093/molbev/msh016 14660702
38. Beiträge zur Anatomie der Gattung Siphonaria. A Köhler, Zoologische Jahrbücher, Abteilung Anatomie 1893 7 1 92
39. The structure and mode of life of the Pyramidellidae, parasitic opisthobranchs. V Fretter A Graham, J Mar Biol Ass UK 1949 28 493 532
40. Origins and relationships of primitive members of the Opisthobranchia (Mollusca: Gastropoda). TM Gosliner, Biol J Linn Soc 1981 16 197 225 10.1111/j.1095-8312.1981.tb01848.x
41. On the central nervous system of Smeagolidae and Rhodopidae, two families questionably allied with the Gymnomorpha (Gastropoda: Euthyneura). G Haszprunar G Huber, J Zool 1990 220 185 199
42. Evolution within the Gastropoda: Prosobranchia. The Mollusca. A Graham, Evolution New York, Academic Press, Trueman ER, Clarke MR, 1985 10 151 186
43. The fine-structure of the mature spermatozoon of Onchidella celtica (Cuvier) (Mollusca, Gastropoda) and its phylogenetic implications. MG Selmi F Giusti G Manganelli, J Ultrastruct Mol Struct Research 1988 99 107 123 10.1016/0889-1605(88)90047-X
44. Relationships of Gymnomorph Gastropods Mollusca Gastropoda. S Tillier, Zool J Linn Soc 1984 82 345 362
45. Testing the utility of partial COI sequences for phylogenetic estimates of gastropod relationships. EA Remigio PDN Hebert, Mol Phylogenet Evol 2003 29 641 647 10.1016/S1055-7903(03)00140-4 14615199
46. Phylogenetic analysis of Euthyneura (Gastropoda) by means of the 16s rRNA gene: use of a fast gene for higher-level phylogenies. M Thollesson, Proc R Soc Lond B 1999 266 75 83 10.1098/rspb.1999.0606
47. Animal mitochondrial genomes. JL Boore, Nucleic Acids Res 1999 27 1767 1780 10101183 10.1093/nar/27.8.1767
48. Complete sequences of the highly rearranged molluscan mitochondrial genomes of the Scaphopod Graptacme eborea and the bivalve Mytilus edulis. JL Boore M Medina LA Rosenberg, Mol Biol Evol 2004 21 1492 1503 10.1093/molbev/msh090 15014161
49. The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica - and the first record for a putative Atpase subunit 8 gene in marine bivalves. H Dreyer G Steiner, Front Zool 2006 3 13 16948842 10.1186/1742-9994-3-13
50. Crassostrea gigas mitochondrial DNA. SH Kim EY Je DW Park, Genbank accession number AF177226 1999
51. Gender-associated mtDNA of Tapes philippinarum. M Okazaki R Ueshima, Genbank accession number NC_003354 2002
52. Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes. S Yokobori N Fukuda M Nakamura T Aoyama T Oshima, Mol Biol Evol 2004 21 2034 2046 10.1093/molbev/msh227 15297602
53. Transfer RNA editing in land snail mitochondria. S Yokobori S Pääbo, Proc Natl Acad Sci USA 1995 92 10432 10435 7479799 10.1073/pnas.92.22.10432
54. Gastropod phylogeny challenges for the 90S. WF Ponder DR Lindberg, Origin and evolutionary radiation of the Mollusca The Malacological Society of London. Oxford University Press, Taylor J, 1996 135 154
55. Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. R Shao M Dowton A Murrell SC Barker, Mol Biol Evol 2003 20 1612 1619 10.1093/molbev/msg176 12832626
56. Partial 28S rDNA sequences and the antiquity of hydrothermal vent endemic gastropods. AG McArthur BF Koop, Mol Phylogenet Evol 1999 13 255 274 10.1006/mpev.1999.0645 10603255
57. Four characters and the higher systematics of gastropods. R Robertson, Am Malac Bull Spetial Ed 1985 1 1 22
58. The Heterobranchia- a new concept of the phylogeny and evolution of the higher Gastropoda. G Haszprunar, Z Zool Syst Evolut-forsch 1985 23 15 37
59. Marine valvatoideans gastropods _ implications for early heterobranch phylogeny. WF Ponder, J Moll Stud 1991 57 21 32 10.1093/mollus/57.1.21
60. Classification of the Caenogastropoda and Heterostropha - a list of the family group names and higher taxa. WF Ponder A Warén, Prosobranch phylogeny Malacological Rev Supp 4, Ponder WF, 1988 288 328
61. A Franc, Traité de Zoologie. Opisthobranches Sect III. Paris, Masson 1968 V
62. An outline of gastropod classification. DW Taylor NF Sohl, Malacologia 1962 1 7 32
63. TE Thompson, Biology of Opisthobranch molluscs London, The Ray Society 1976 I
64. Recherches morphologiques et phylogénétiques sur les Mollusques Archaïques. P Pelseneer, Memoires couronnés et Memoires des savants etrangés, l'Academie Royale des Sciences de Belgique 1899 57 1 112 I-XXIV
65. The Invertebrates. LH Hyman, Mollusca I New York, McGraw-Hill 1967 6 1 792
66. Zum cerebralen Nervensystem mariner Heterobranchia (Gastropoda). G Huber, Dissertation am Institut für Zoologie der Universität Wien, Wien, Austria 1987
67. Étude morphologique et phylogénétique du ganglion cérébroide des gastéropodes pulmonés (mollusques). JJ van Mol, Mém Acad r Belg Cl Sci 1967 37 1 168
68. Evolution phylogénétique du ganglion céré broide chez les gastéropodes pulmonés. JJ van Mol, Haliotis 1974 4 77 86
69. GM Barker, The biology of terrestrial molluscs Hamilton, New Zealand, CABI publishing 2001
70. Zur systematischen Stellung von Soleolifera und Rhodope (Gastropoda, Euthyneura). L Salvini-Plawen, Zoologisches Jahrbuch für Systematik 1970 97 285 299
71. Gene arrangement in sea star mitochondrial DNA demonstrates a major inversion event during echinoderm evolution. MJ Smith DK Banfield K Doteval S Gorski DJ Kowbel, Gene 1989 76 181 185 10.1016/0378-1119(89)90022-X 2744480
72. Animal mitochondrial DNA recombination. DH Lunt BC Hyman, Nature 1997 387 247 10.1038/387247a0 9153388
73. Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. C Moritz WM Brown, Proc Natl Acad Sci USA 1987 84 7183 7187 3478691 10.1073/pnas.84.20.7183
74. Tandem duplication via light-strand synthesis may provide a precursor for mitochondrial genomic rearrangement. JR Macey JA Schulte 2nd A Larson TJ Papenfuss, Mol Biol Evol 1998 15 71 75 9491606
75. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. TA Rawlings TM Collins R Bieler, Proc Natl Acad Sci USA 2003 100 15700 15705 14673095 10.1073/pnas.2535036100
76. Molecular Cloning. J Sambrook EF Fritsch T Maniatis, A Laboratory Manual Cold Spring Harbor, NY, Cold Spring Harbor Laboratory Press 1989
77. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. O Folmer M Black W Hoeh R Lutz R Vrijenhoek, Mol Mar Biol Biotech 1994 3 294 299
78. S Palumbi A Martin S Romano WO McMillan L Stice G Grabowwski, The simple fool's guide to PCR. Version 2.0 Honolulu, HL 96822, Department of Zoology and Kewalo Marine Laborator, University of Hawaii 1991
79. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. TD Kocher WK Thomas A Meyer SV Edwards S Paabo FX Villablanca AC Wilson, Proc Natl Acad Sci USA 1989 86 16 6196 6200 2762322 10.1073/pnas.86.16.6196
80. Protein Database Searches for Multiple Alignments. SF Altschul DJ Lipman, Proc Natl Acad Sci USA 1990 87 5509 5513 2196570 10.1073/pnas.87.14.5509
81. WP Maddison DR Maddison, MacClade: Analysis of phylogeny and character evolution Sinauer Associates, Sunderland, MA 1992
82. DL Swofford, PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0 Sunderland, MA, Sinauer Associates 2002
83. Gene content and organization of a mitochondrial DNA segment of the squid Loligo bleekeri. J Sasuga S Yokobori M Kaifu T Ueda K Nishikawa K Watanave, J Mol Evol 1999 48 692 702 10.1007/PL00006513 10229573
84. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. JL Boore WM Brown, Genetics 1994 138 423 443 7828825
85. The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids Res 1997 25 4876 4882 9396791 10.1093/nar/25.24.4876
86. A simple method for estimating and testing minimum-evolution trees. A Rzhetsky M Nei, Mol Biol Evol 1992 9 945 967
87. Confidence limits on phylogenies: an approach using the bootstrap. J Felsenstein, Evolution 1985 39 783 791 10.2307/2408678
88. ProtTest: selection of best-fit models of protein evolution. F Abascal R Zardoya D Posada, Bioinformatics 2005 21 2104 2105 10.1093/bioinformatics/bti263 15647292
89. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. S Whelan N Goldman, Mol Biol Evol 2001 18 691 699 11319253
90. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 696 704 10.1080/10635150390235520 14530136
91. MrBayes: Bayesian inference of phylogeny. JP Huelsenbeck FR Ronquist, Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754 11524383
92. An approximately unbiased test of phylogenetic tree selection. H Shimodaira, Syst Biol 2002 51 492 508 10.1080/10635150290069913 12079646
93. CONSEL: for assessing the confidence of phylogenetic tree selection. H Shimodaira M Hasegawa, Bioinformatics 2001 17 1246 1247 10.1093/bioinformatics/ 17.12.1246 11751242
94. BADGER, version 1.02b. Department of Mathematics and Computer Science, Duquesne University. DL Simon B Larget, 2004 http://badger.duq.edu/