Divergence of the mitochondrial genome structure in the apicomplexan parasites, babesia and theileria

Molecular Biology and Evolution

Volumn 27, Issue 5, 2010, Pages 1107-1116

  Hikosaka, Kenji ^a   Watanabe, Yoh Ichi ^b   Tsuji, Naotoshi ^c   Kita, Kiyoshi ^b   Kishine, Hiroe ^a   Arisue, Nobuko ^a   Palacpac, Nirianne Marie Q ^a   Kawazu, Shin Ichiro ^d   Sawai, Hiromi ^a   Horii, Toshihiro ^a   Igarashi, Ikuo ^d   Tanabe, Kazuyuki ^a  

^a OSAKA UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c NATIONAL INSTITUTE OF ANIMAL HEALTH   (Japan)

^d OBIHIRO UNIVERSITY OF AGRICULTURE AND VETERINARY MEDICINE   (Japan)

Author keywords

Apicomplexa; Babesia; Mitochondrial genome; Mitochondrion; Plasmodium; Theileria

Indexed keywords

LARGE SUBUNIT RIBOSOMAL RNA;

AMINO ACID SEQUENCE; APICOMPLEXA; ARTICLE; BABESIA; BABESIA BIGEMINA; BABESIA BOVIS; BABESIA CABALLI; BABESIA EQUI; BABESIA GIBSONI; COB GENE; COX 1 GENE; COX 3 GENE; GENE; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; INVERTED REPEAT; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM; RNA GENE; SEQUENCE ANALYSIS; SYNTENY; TANDEM REPEAT; THEILERIA; THEILERIA ANNULATA; THEILERIA ORIENTALIS; THEILERIA PARVA;

ANIMALS; BABESIA; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, INTERGENIC; GENETIC VARIATION; GENOME, MITOCHONDRIAL; GENOME, PROTOZOAN; LIKELIHOOD FUNCTIONS; OPEN READING FRAMES; PARASITES; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID; THEILERIA; TRANSCRIPTION, GENETIC;

APICOMPLEXA; BABESIA; BABESIA BIGEMINA; BABESIA BOVIS; BABESIA CABALLI; BABESIA GIBSONI; PLASMODIUM (APICOMPLEXA); THEILERIA; THEILERIA ANNULATA; THEILERIA EQUI; THEILERIA ORIENTALIS; THEILERIA PARVA;

EID: 77951598028     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp320     Document Type: Article

References (47)

1. Abrahamsen MS, Templeton TJ, Enomoto S, et al. (20 co-authors). 2004. Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 304:441-445.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
3. Avarzed A, Igarashi I, De Waal DT, et al. (12 co-authors). 1998. Monoclonal antibody against Babesia equi: characterization and potential application of antigen for serodiagnosis. J Clin Microbiol. 36:1835-1839.
4. Avarzed A, Igarashi I, Kanemaru T, Hirumi K, Omata Y, Saito A, Oyamada T, Nagasawa H, Toyoda Y, Suzuki N. 1997. Improved in vitro cultivation of Babesia caballi. J Vet Med Sci. 59:479-481.
5. Bah A, Bachand F, Clair E, Autexier C, Wellinger RJ. 2004. Humanized telomeres and an attempt to express a functional human telomerase in yeast. Nucleic Acids Res. 32:1917-1927.
6. Brayton KA, Lau AO, Herndon DR, et al. (28 co-authors). 2007. Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog. 3:1401-1413.
7. Brown T, Mackey K, Du T. 2004. Analysis of RNA by northern and slot blot hybridization. Curr Protoc Mol Biol. 49:1-19.
8. Castresana J, Lubben M, Saraste M, Higgins DG. 1994. Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen. Embo J. 13:2516-2525.
9. Criado-Fornelio A, Martinez-Marcos A, Buling-Sarana A, Barba-Carretero JC. 2003. Molecular studies on Babesia, Theileria and Hepatozoon in southern Europe. Part II. Phylogenetic analysis and evolutionary history. Vet Parasitol. 114:173-194.
10. Feagin JE, Mericle BL, Werner E, Morris M. 1997. Identification of additional rRNA fragments encoded by the Plasmodium falciparum 6 kb element. Nucleic Acids Res. 25:438-446.
11. Felsenstein J, Churchill GA. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol. 13:93-104.
12. Ferguson-Miller S, Babcock GT. 1996. Heme/copper terminal oxidases. Chem Rev. 96:2889-2908.
13. Freyhult EK, Bollback JP, Gardner PP. 2007. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res. 17:117-125.
14. Fujinaga T, Minami T, Ishihara T. 1980. Serological relationship between a large Babesia found in Japanese cattle and Babesia major, B. bigemina and B. bovis. Res Vet Sci. 29:230-234.
15. Gray MW, Lang BF, Burger G. 2004. Mitochondria of protists. Annu Rev Genet. 38:477-524.
16. Hall R, Coggins L, McKellar S, Shiels B, Tait A. 1990. Characterisation of an extrachromosomal DNA element from Theileria annulata. Mol Biochem Parasitol. 38:253-260.
17. Haltia T, Saraste M, Wikstrom M. 1991. Subunit III of cytochrome c oxidase is not involved in proton translocation: a site-directed mutagenesis study. Embo J. 10:2015-2021.
18. Ishimine T, Makimura S, Kitazawa S, Tamura S, Suzuki N. 1978. Pathophysiological findings on blood of beagles experimentally infected with B. gibsoni. Jpn J Trop Med Hyg. 6:15-26.
19. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
20. Kairo A, Fairlamb AH, Gobright E, Nene V. 1994. A 7.1 kb linear DNA molecule of Theileria parva has scrambled rDNA sequences and open reading frames for mitochondrially encoded proteins. Embo J. 13:898-905.
21. Kim JY, Yokoyama N, Kumar S, Inoue N, Inaba M, Fujisaki K, Sugimoto C. 2004. Identification of a piroplasm protein of Theileria orientalis that binds to bovine erythrocyte band 3. Mol Biochem Parasitol. 137:193-200.
22. Kishino H, Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol. 29:170-179.
23. Kuo CH, Wares JP, Kissinger JC. 2008. The apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees. Mol Biol Evol. 25:2689-2698.
24. Lau AO. 2009. An overview of the Babesia, Plasmodium and Theileria genomes: a comparative perspective. Mol Biochem Parasitol. 164:1-8.
25. Levine ND. 1988. Progress in taxonomy of the apicomplexan protozoa. J Protozool. 35:518-520.
26. Nosek J, Tomaska L. 2003. Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy. Curr Genet. 44:73-84.
27. Ossorio PN, Sibley LD, Boothroyd JC. 1991. Mitochondrial-like DNA sequences flanked by direct and inverted repeats in the nuclear genome of Toxoplasma gondii. J Mol Biol. 222:525-536.
28. Page RD. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 12:357-358.
29. Palmer JD, Soltis D, Soltis P. 1992. Large size and complex structure of mitochondrial DNA in two nonflowering land plants. Curr Genet. 21:125-129.
30. Pearson WR. 1991. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11:635-650.
31. Perkins SL. 2008. Molecular systematics of the three mitochondrial protein-coding genes of malaria parasites: corroborative and new evidence for the origins of human malaria. Mitochondrial DNA. 19:471-478.
32. Posada D, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
33. Preiser PR, Wilson RJ, Moore PW, McCready S, Hajibagheri MA, Blight KJ, Strath M, Williamson DH. 1996. Recombination associated with replication of malarial mitochondrial DNA. Embo J. 15:684-693.
34. Roshan U, Chikkagoudar S, Livesay DR. 2008. Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinfor-matics. 9:61.
35. Shimodaira H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol. 16:1114-1116.
36. Shukla GC, Nene V. 1998. Telomeric features of Theileria parva mitochondrial DNA derived from cycle sequence data of total genomic DNA. Mol Biochem Parasitol. 95:159-163.
37. Smith DR, Lee RW. 2008. Mitochondrial genome of the colorless green alga Polytomella capuana: a linear molecule with an unprecedented GC content. Mol Biol Evol. 25:487-496.
38. Swofford DL. 2002. PAUP*: phylogenetic analysis using parsimony (and other methods). Sunderland (MA): Sinauer Associates.
39. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: 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. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. 1996. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science 272:1136-1144.
41. Uilenberg G. 2006. Babesia\a historical overview. Vet Parasitol. 138:3-10.
42. Ward BL, Anderson RS, Bendich AJ. 1981. The mitochondrial genome is large and variable in a family of plants (Cucurbita-ceae). Cell 25:793-803.
43. 6-f complex: position of the cytochrome b hemes in the membrane. Proc Natl Acad Sci USA. 81:674-678.
44. Wilson RJ, Williamson DH. 1997. Extrachromosomal DNA in the Apicomplexa. Microbiol Mol Biol Rev. 61:1-16.
45. 1complex from bovine heart mitochondria. Science 277:60-66.
46. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
47. 1complex from Rhodobacter sphaeroides by site-directed mutagenesis. Biochemistry 30:6747-6754.