Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae

Current Genetics

Volumn 51, Issue 5, 2007, Pages 285-296

  Martin, Frank N ^a   Bensasson, Douda ^b,e   Tyler, Brett M ^c   Boore, Jeffrey L ^b,d,f  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF MANCHESTER   (United Kingdom)

^f SymBio Corporation   (United States)

Author keywords

Inverted repeat; Mitochondrial microsatellite; Phytophthora infestans

Indexed keywords

FUNGAL RNA; GENOMIC DNA; METHIONINE TRANSFER RNA; MICROSATELLITE DNA; REPETITIVE DNA; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; DNA SEQUENCE; FUNGAL GENE; FUNGAL GENETICS; GENE MAPPING; GENE ORDER; GENETIC CONSERVATION; GENETIC ORGANIZATION; GENOME ANALYSIS; GENOME SIZE; GENOMICS; INVERTED REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OOMYCETES; OPEN READING FRAME; PHYTOPHTHORA; PHYTOPHTHORA INFESTANS; PHYTOPHTHORA RAMORUM; PHYTOPHTHORA SOJAE; PRIORITY JOURNAL; STRAIN DIFFERENCE;

GENES, MITOCHONDRIAL; GENOME; GENOMICS; MITOCHONDRIA; PHYTOPHTHORA; REPETITIVE SEQUENCES, NUCLEIC ACID;

OOMYCETES; PHYTOPHTHORA; PHYTOPHTHORA INFESTANS; PHYTOPHTHORA RAMORUM; PHYTOPHTHORA SOJAE;

EID: 34247223751     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-007-0121-6     Document Type: Article

References (43)

1. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310
2. Avila-Adame C, Gomez-Alpizar L, Zismann V, Jones KM, Buell CR, Beagle Ristaino J (2006) Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Curr Genet 49:39-46
3. Baldauf SL, Palmer JD (1993) Animals and fungi are each other's closest relatives: Congruent evidence from multiple proteins. Proc Natl Acad Sci USA 90:11558-11562
4. Bhattacharya D, Stickel SK (1994) Sequence analysis of duplicated actin genes in Lagenidium giganteum and Pythium irregulare (Oomycota). J Mol Evol 39:56-61
5. Boyd DA, Hobman TC, Gruenke SA, Klassen GR (1984) Evolutionary stability of mitochondrial DNA organization in Achlya. Can J Biochem Cell Biol 62:571-576
6. Brasier CM, Denman S, Brown A, Webber J (2005) Sudden oak death (Phytophthora ramorum) discovered in trees in Europe. Mycol Res 108:1108-1110
7. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S (2003) NISC comparative sequencing program. Lagan and multi-lagan: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13:721-731
8. Chesnick JM, Goff M, Graham J, Ocampo C, Lang BF, Seif E, Burger G (2000) The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization. Nucleic Acids Res 28:2512-2518
9. Cooke DEL, Drenth A, Duncan JM, Wagels G, Brasier CM (2000) A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet Biol 30:17-32
10. Davidson JM, Werres S, Garbelotto M, Hanson E, Rizzo DM (2003) Sudden oak death and associated diseases caused by Phytophthora ramorum. Plant Health Prog. doi:10.1094/PHP-2003-0707-01-DG
11. Dick MW (2001) Straminipilous fungi. Kluwer, Hingham, MA
12. Erwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide. American Phytopathological Society Press St. Paul, MN, 562 pp
13. Förster H, Coffey MD, Elwood H, Sogin ML (1990) Sequence analysis of the small subunit ribosomal RNAs of three zoosporic fungi and implications for fungal evolution. Mycologia 82:306-312
14. Förster H, Kinscherf TG, Leong S, Maxwell DP (1987) Molecular analysis of the mitochondrial genome of Phytophthora. Curr Genet 12:215-218
15. Förster H, Kinscherf TG, Leong S, Maxwell DP (1988) Estimation of relatedness between phytophthora species by analysis of mitochondrial DNA. Mycologia 80:466-478
16. Förster H, Kinscherf TG, Leong S, Maxwell DP (1989) Restriction fragment length polymorphism of the mitochondrial DNA of phytophthora megasperma isolated form soybean, alfalfa, and fruit trees. Can J Bot 67:529-537
17. Förster H, Tyler BM, Coffey MD (1994) Phytophthora sojae races have arisen by clonal evolution and by rare outcrosses. Mol Plant Microbe Interact 7:780-791
18. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32 (web server issue):W273-W279
19. Gray MW, Lang BF, Cedergren R, Golding G, Lemieux C, Sankoff D, Turmel M, Brossard N, Delage E, Littlejohn TG, Plante I, Rioux P, Saint-Louis D, Zhu Y, Burger G (1998) Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res 26: 865-878
20. Grayburn WS, Hudspeth DSS, Gane MK, Hudspeth MES (2004) The mitochondrial genome of Saprolegnia ferax: Organization, gene content, and nucleotide sequence. Mycologia 96:980-987
21. Hudspeth MES, Shumard DS, Bradford JR, Grossman LI (1983) Organization of Achlya mtDNA: A population with two orientation and a large inverted repeat containing the rRNA genes. Proc Natl Acad Sci USA 80:142-146
22. Knoll HA (1992) The early evolution of eukaryotes: A geological perspective. Science 256:622-627
23. Kroon LPNM, Bakker FT, van den Bosch GB, Bonnants PJ, Flier WG (2004) Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Genet Biol 41:766-782
24. Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955-964
25. Martin FN (1991) Linear mitochondrial molecules and intraspecific mitochondrial genome stability in a species of Pythium. Genome 34:156-162
26. Martin FN (2000) Phylogenetic relationships among some Pythium species inferred from sequence analysis of the mitochondrially encoded cytochrome oxidase II gene. Mycologia 92:711-727
27. Martin FN, Tooley PW (2003a) Phylogenetic relationships among Phytophthora species inferred from sequence analysis of the mitochondrially-encoded cytochrome oxidase I and II genes. Mycologia 95:269-284
28. Martin FN, Tooley PW (2003b) Phylogenetic relationships of Phytophthora ramorum, P. nemorosa, and P. pseudosyringae, three species recovered from areas in California with sudden oak death. Mycol Res 107:1379-1391
29. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I (2000) VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16:1046
30. McNabb SA, Boyd DA, Belkhiri A, Dick MW, Klassen GR (1987) An inverted repeat comprises more than three quarters of the mitochondrial genome in two species of Pythium. Curr Genet 12:205-208
31. McNabb SA, Klassen GR (1988) Uniformity of mitochondrial DNA complexity in Oomycetes and the evolution of the inverted repeat. Exp Mycol 12:233-242
32. McNabb SA, Eros RW, Klassen GR (1988) Presence and absence of large inverted repeats in the mitochondrial DNA of hyphochytriomycetes. Can J Bot 66:2377-2379
33. Oudot-Le Sec M-P, Loiseaux-de Goër S, Stam WT, Olsen JL (2006) Complete mitochondrial genomes of the three brown algae (heterokonta: phaeophyceae) Dictyota dichotomam, Fucus vesiculosus and Desmarestia viridis. Curr Genet 49:47-58
34. Paquin B, Laforest M-J, Forget L, Roewer I, Wang Z, Longcore J, Lang BF (1997) The fungal mitochondrial genome project: Evolution of fungal mitochondrial genomes and their gene expression. Curr Genet 31:380-395
35. Rizzo DM, Garbelotto M, Davidson JM, Slaughter GW, Koike ST (2002) Phytophthora ramorum as the cause of extensive mortality of Quercus spp. and Lithocarpus densiflorus in California. Plant Dis 86:205-214
36. Shumard-Hudspeth DS, Hudspeth MES (1990) Genetic rearrangements in Phytophthora mitochondrial DNA. Curr Genet 17:413-415
37. Shumard DS, Grossman LI, Hudspeth MES (1986) Achlya mitochondrial DNA: gene localization and analysis of inverted repeats. Mol Gen Genet 202:16-23
38. Tyler BM, Tripathi S, Zhang X, Dehal P, Jiang R, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon J, Chapman J, Damasceno CMB, Dorrance AE, Dou D, Dickerman AW, Dubchak I, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors K, Jones RW, Kamoun S, Krampis K, Lamour K, Lee M-K, McDonald WH, Medina M, Meijer HJG, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris P, Phuntumart V, Putnam N, Rash S, Rose JKC, Sakihama Y, Salamov A, Savidor A, Scheuring CF, Smith BM, Sobral BWS, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev I, Rokhsar D, Boore JL (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313:1261-1266
39. Wainright PO, Hinkle G, Sogin ML, Stickel SK (1993) Monophyletic origins of the metazoa: An evolutionary link with fungi. Science 260:340-342
40. Weerakoon ND, Roberts JK, Lehnen LP, Hardham AR (1998) Isolation and characterization of the single β-tublin gene in Phytophthora cinnamomi. Mycologia 90:85-95
41. Werres S, Marwitz R, Man In'T Veld WA, Cock AWAM, Bonants PJM, Weerdt Md, Themann K, Ilieva E, Baayen RP (2001) Phytophthora ramorum sp. nov., a new pathogen on Rhododendron and viburnum. Mycol Res 105:1155-1165
42. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
43. Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32-43