Sessile snails, dynamic genomes: Gene rearrangements within the mitochondrial genome of a family of caenogastropod molluscs

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Rawlings, Timothy A ^a   MacInnis, Martin J ^a,b   Bieler, Rüdiger ^c   Boore, Jeffrey L ^d   Collins, Timothy M ^e,f  

^a CAPE BRETON UNIVERSITY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c FIELD MUSEUM OF NATURAL HISTORY   (United States)

^d Genome Project Solutions   (United States)

^e FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^f NATIONAL SCIENCE FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; DENDROPOMA GREGARIUM; DENDROPOMA MAXIMUM; EUALETES TULIPA; GASTROPOD; GENE DUPLICATION; GENE ORDER; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC SIMILARITY; GENOME ANALYSIS; MITOCHONDRIAL GENOME; MOLLUSC; MORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PSEUDOGENE; SESSILE SPECIES; SNAIL; SPERM; TAXONOMY; THYLACODES SQUAMIGREUS; THYLAEODUS; VERMETUS ERECTUS; ANIMAL; CLASSIFICATION; CODON; DNA BASE COMPOSITION; GENETICS; GENOMICS; MOLECULAR GENETICS; PHYSIOLOGY;

ANIMALIA; CAENOGASTROPODA; DENDROPOMA MAXIMUM; GASTROPODA; LITTORINIMORPHA; MOLLUSCA; TULIPA; VERMETIDAE; VERMETUS; VERTEBRATA;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CODON; GENE DUPLICATION; GENE ORDER; GENE REARRANGEMENT; GENOME, MITOCHONDRIAL; GENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, TRANSFER; SNAILS;

EID: 77954662929     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-440     Document Type: Article

References (63)

1. Boore JL. Animal mitochondrial genomes. Nucleic Acids Research 1999, 27(8):1767-1780. 10.1093/nar/27.8.1767, 148383, 10101183.
2. Smith MJ, Arndt A, Gorski S, Fajber E. The phylogeny of echinoderm classes based on mitochondrial gene arrangements. Journal of Molecular Evolution 1993, 36:545-554.
3. Boore JL, Brown WM. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics 1995, 141:305-319. 1206728, 8536978.
4. Lavrov DV, Brown WM, Boore JL. Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings of the Royal Society of London Series B-Biological Sciences 2004, 271(1538):537-544.
5. Boore JL, Brown WM. Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Molecular Biology and Evolution 2000, 17(1):87-106.
6. Lavrov DV, Lang BF. Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements. Systematic Biology 2005, 54(4):651-659. 10.1080/10635150500221044, 16126659.
7. Boore JL, Macey JR, Medina M. Sequencing and comparing whole mitochondrial genomes of animals. Methods in Enzymology 2005, 395:311-348. full_text, 15865975.
8. Simison WB, Lindberg DR, Boore JL. Rolling circle amplification of metazoan mitochondrial genomes. Molecular Phylogenetics and Evolution 2006, 39(2):562-567. 10.1016/j.ympev.2005.11.006, 16360323.
9. Hudson ME. Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 2007, 8:3-17.
10. Blanchette M, Kunisawa T, Sankoff D. Gene order breakpoint evidence in animal mitochondrial phylogeny. Journal of Molecular Evolution 1999, 49(2):193-203. 10.1007/PL00006542, 10441671.
11. Moret BME, Tang JJ, Wang LS, Warnow T. Steps toward accurate reconstructions of phylogenies from gene-order data. Journal of Computer and System Sciences 2002, 65(3):508-525.
12. Larget B, Simon DL, Kadane JB, Sweet D. A Bayesian analysis of metazoan mitochondrial genome arrangements. Molecular Biology and Evolution 2005, 22(3):486-495. 10.1093/molbev/msi032, 15525697.
13. Simison WB, Boore JL. Molluscan evolutionary genomics. Phylogeny and Evolution of the Mollusca 2008, 447-461. Berkeley, CA: University of California Press, Ponder W, Lindberg DR.
14. Vallès Y, Boore JL. Lophotrochozoan mitochondrial genomes. Integrative and Comparative Biology 2006, 46(4):544-557.
15. Grande C, Templado J, Zardoya R. Evolution of gastropod mitochondrial genome arrangements. BMC Evolutionary Biology 2008, 8. 10.1186/1471-2148-8-61, 2291457, 18302768.
16. Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 2008, 101(4):301-320. 10.1038/hdy.2008.62, 18612321.
17. Milbury CA, Gaffney PM. Complete mitochondrial DNA sequence of the eastern oyster Crassostrea virginica. Marine Biotechnology 2005, 7(6):697-712. 10.1007/s10126-005-0004-0, 16132463.
18. Rawlings TA, Collins TM, Bieler R. A major mitochondrial gene rearrangement among closely related species. Molecular Biology and Evolution 2001, 18(8):1604-1609.
19. Serb JM, Lydeard C. Complete mtDNA Sequence of the North American Freshwater Mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca). Molecular Biology and Evolution 2003, 20(11):1854-1866. 10.1093/molbev/msg218, 12949150.
20. Dowton M, Castro LR, Austin AD. Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'. Invertebrate Systematics 2002, 16(3):345-356.
21. Ballard JWO, Rand DM. The population biology of mitochondrial DNA and its phylogenetic implications. Annual Review of Ecology Evolution and Systematics 2005, 36:621-642.
22. Levinson G, Gutman GA. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution 1987, 4(3):203-221.
23. Boore JL, Brown WM. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics & Development 1998, 8(6):668-674. 10.1016/S0959-437X(98)80035-X, 15734570, 9914213.
24. Lunt DH, Hyman BC. Animal mitochondrial DNA recombination. Nature 1997, 387:247. 10.1038/387247a0, 9153388.
25. Cantatore P, Gadaleta MN, Roberti M, Saccone C, Wilson AC. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 1987, 329:853-855. 10.1038/329853a0, 3670390.
26. Higgs PG, Jameson D, Jow H, Rattray M. The evolution of tRNA-Leu genes in animal mitochondrial genomes. Journal of Molecular Evolution 2003, 57(4):435-445. 10.1007/s00239-003-2494-6, 14708576.
27. Lavrov DV, Lang BF. Transfer RNA gene recruitment in mitochondrial DNA. Trends in Genetics 2005, 21(3):129-133. 10.1016/j.tig.2005.01.004, 15734570.
28. Rawlings TA, Collins TM, Bieler R. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America 2003, 100(26):15700-15705. 10.1073/pnas.2535036100, 307631, 14673095.
29. Dowton M, Austin AD. Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the Hymenoptera. Molecular Biology and Evolution 1999, 16(2):298-309.
30. San Mauro D, Gower DJ, Zardoya R, Wilkinson M. A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Molecular Biology and Evolution 2006, 23(1):227-234. 10.1093/molbev/msj025, 16177229.
31. Lavrov DV, Boore JL, Brown WM. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and nonrandom loss. Molecular Biology and Evolution 2002, 19(2):163-169.
32. Flook P, Rowell H, Gellissen G. Homoplastic rearrangements of insect mitochondrial transfer-RNA genes. Naturwissenschaften 1995, 82(7):336-337.
33. Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Molecular Phylogenetics and Evolution 2004, 33(1):22-31. 10.1016/j.ympev.2004.05.003, 15324836.
34. Dowton M, Cameron SL, Dowavic JI, Austin AD, Whiting MF. Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral. Molecular Biology and Evolution 2009, 26(7):1607-1617. 10.1093/molbev/msp072, 19359443.
35. Iannelli F, Griggio F, Pesole G, Gissi C. The mitochondrial genome of Phallusia mammillata and Phallusia fumigata (Tunicata, Ascidiacea): high genome plasticity at intra-genus level. BMC Evolutionary Biology 2007, 7. 10.1186/1471-2148-7-155, 2220002, 17764550.
36. Ponder WF, Lindberg DR. Towards a phylogeny of gastropod molluscs: an analysis using morphological characters. Zoological Journal of the Linnean Society 1997, 119:83-265.
37. Colgan DJ, Ponder WF, Beacham E, Macaranas J. Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca). Molecular Phylogenetics and Evolution 2007, 42(3):717-737. 10.1016/j.ympev.2006.10.009, 17127080.
38. Healy JM. Sperm morphology in Serpulorbis and Dendropoma and its relevance to the systematic position of the Vermetidae. Journal of Molluscan Studies 1988, 54:295-308.
39. Collins TM, Frazer KS, Palmer AR, Vermeij GJ, Brown WM. Evolutionary history of Northern Hemisphere Nucella: molecules, morphology, ecology, and fossils. Evolution 1996, 50:2287-2304.
40. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 1994, 3(5):294-299.
41. Boore JL. The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics 2006, 7. 10.1186/1471-2164-7-182, 1544340, 16854241.
42. Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 1997, 25(5):955-964. 10.1093/nar/25.5.955, 146525, 9023104.
43. Laslett D, Canback B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24(2):172-175. 10.1093/bioinformatics/btm573, 18033792.
44. Perna NT, Kocher TD. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution 1995, 41(3):353-358. 10.1007/BF01215182, 7563121.
45. Reyes A, Gissi C, Pesole G, Saccone C. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Molecular Biology and Evolution 1998, 15(8):957-966.
46. Santos MAS, Moura G, Massey SE, Tuite MF. Driving change: the evolution of alternative genetic codes. Trends in Genetics 2004, 20(2):95-102. 10.1016/j.tig.2003.12.009, 14746991.
47. Yokobori S, Suzuki T, Watanabe K. Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. Journal of Molecular Evolution 2001, 53:(4-5):314-326.
48. Bandyopadhyay PK, Stevenson BJ, Cady MT, Olivera BM, Wolstenholme DR. Complete mitochondrial DNA sequence of a Conoidean gastropod, Lophiotoma (Xenuroturris) cerithiformis: gene order and gastropod phylogeny. Toxicon 2006, 48(1):29-43. 10.1016/j.toxicon.2006.04.013, 16806344.
49. Boore JL, Daehler LL, Brown WM. Complete sequence, gene arrangement, and genetic code of mitochondrial DNA of the cephalochordate Branchiostoma floridae (Amphioxus). Molecular Biology and Evolution 1999, 16(3):410-418.
50. Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology: 1994; Menlo Park, California 1994, 28-36. AAAI Press.
51. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
52. Bandyopadhyay PK, Stevenson BJ, Ownby JP, Cady MT, Watkins M, Olivera BM. The mitochondrial genome of Conus textile, coxI-coxII intergenic sequences and conoidean evolution. Molecular Phylogenetics and Evolution 2008, 46(1):215-223. 10.1016/j.ympev.2007.08.002, 2718723, 17936021.
53. Cunha RL, Grande C, Zardoya R. Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evolutionary Biology 2009, 9:210. 10.1186/1471-2148-9-210, 2741453, 19698157.
54. Jang KH, Hwang UW. Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa. BMC Genomics 2009, 10. 10.1186/1471-2164-10-167, 2678162, 19379522.
55. Boore JL, Brown WM. Complete DNA-sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics 1994, 138(2):423-443. 1206160, 7828825.
56. Maynard BT, Kerr LJ, McKiernan JM, Jansen ES, Hanna PJ. Mitochondrial DNA sequence and gene organization in the Australian Blacklip Abalone Haliotis rubra (Leach). Marine Biotechnology 2005, 7:645-658. 10.1007/s10126-005-0013-z, 16206015.
57. Wang X, Lavrov DV. Seventeen new complete mtDNA sequences reveal extensive mitochondrial genome evolution within the Demospongiae. Public Library of Science One 2008, 3(7):e2723. 2444032, 18628961.
58. Brugler MR, France SC. The mitochondrial genome of a deep-sea bamboo coral (Cnidaria, Anthozoa, Octocorallia, Isididae): genome structure and putative origins of replication are not conserved among octocorals. Journal of Molecular Evolution 2008, 67(2):125-136. 10.1007/s00239-008-9116-2, 18506498.
59. Arunkumar KP, Nagaraju J. Unusually long palindromes are abundant in mitochondrial control regions of insects and nematodes. Public Library of Science One 2006, 1(1):e110. 1762429, 17205114.
60. Saito S, Tamura K, Aotsuka T. Replication origin of mitochondrial DNA in insects. Genetics 2005, 171(4):1695-1705. 10.1534/genetics.105.046243, 1456096, 16118189.
61. Lavrov DV, Brown WM. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structures tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics 2001, 157(2):621-637. 1461501, 11156984.
62. Bieler R, Petit RE. Thylacodes - Thylacodus - Tulaxodus: Worm-snail name confusion and the status of Serpulorbis (Gastropoda: Vermetidae). Malacologia 2010, 52(1):183-187.
63. Lupi R, D'Onorio de Meo P, Picardi E, D'Antonio M, Paoletti D, Castrignano T, Pesole G, Gissi C. MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion 2010, 10(2):192-199. 10.1016/j.mito.2010.01.004, 20080208.