Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Amyotte, Stefan G ^a   Tan, Xiaoping ^b   Pennerman, Kayla ^b   del Mar Jimenez Gasco, Maria ^c   Klosterman, Steven J ^d   Ma, Li Jun ^e   Dobinson, Katherine F ^a,f   Veronese, Paola ^b  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e UNIVERSITY OF MASSACHUSETTS   (United States)

^f AGRICULTURE AND AGRI FOOD CANADA   (Canada)

Author keywords

DNA transposons; Genome evolution; Repeat induced point mutation (RIP); Retrotransposons; TE domestication; Transposable elements; Verticillium spp.

Indexed keywords

ARTICLE; CARBOXY TERMINAL SEQUENCE; CONSENSUS SEQUENCE; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FUNGAL GENOME; FUNGAL STRAIN; FUNGUS ISOLATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; POINT MUTATION; PROTEIN DOMAIN; PROTEIN MOTIF; RETROPOSON; TRANSPOSON; VERTICILLIUM; VERTICILLIUM ALBO ATRUM; VERTICILLIUM DAHLIAE;

COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENETIC LINKAGE; GENOME, FUNGAL; OPEN READING FRAMES; PHYLOGENY; RETROELEMENTS; VERTICILLIUM;

FUNGI; VERTICILLIUM ALBO-ATRUM; VERTICILLIUM DAHLIAE;

EID: 84866153660     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-314     Document Type: Article

References (84)

1. Pegg GF, Brady BL. Verticillium wilts 2002, CABI Publishing, New York.
2. Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BPHJ, Chen Z, Henrissat B, Lee Y-H, Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta A, de Jonge R, Santhanam P, Maruthachalam K, Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma L-J. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathogens 2011, 7:e1002137. 10.1371/journal.ppat.1002137, 3145793, 21829347.
3. Dobinson KF, Patterson NA, White GJ, Grant S. DNA fingerprinting and vegetative compatibility analysis indicate multiple origins for Verticillium dahliae race 2 tomato isolates from Ontario, Canada. Mycol Res 1998, 102:1089-1095.
4. Usami T, Shishido M, Ebihara Y, Kamigahira Y, Amemiya Y. Retrotransposon-like elements in the genome of Verticillium dahliae may be used as DNA markers for fungal species and pathotypes. J Gen Plant Pathol 2005, 71:117-123.
5. Feshotte C. The contribution of transposable elements to the evolution of regulatory networks. Nat Rev Genet 2008, 9:397-405. 10.1038/nrg2337, 2596197, 18368054.
6. Bourque G. Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr Opinion Gen & Dev 2009, 19:607-612. 10.1016/j.gde.2009.10.013, 15708420.
7. Shapiro JA. Mobile DNA and evolution in the 21th century. Mob DNA 2010, 1:1-14. 10.1186/1759-8753-1-1, 2836004, 20226071.
8. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007, 8:973-982. 10.1038/nrg2165, 17984973.
9. Kapitonov VV, Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 2008, 9:411-412.
10. Kapitonov VV, Jurka J. Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA 2001, 98:8714-8719. 10.1073/pnas.151269298, 37501, 11447285.
11. Pritham EJ, Putliwala T, Feschotte C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 2007, 390:3-17. 10.1016/j.gene.2006.08.008, 17034960.
12. Hua-Van A, Le Rouzic A, Boutin TS, Filee J, Capy P. The struggle for life of the genome's selfish architects. Biol Direct 2011, 6.
13. Thon M, Pan H, Diener S, Papalas J, Taro A, Mitchell T, Dean R. The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol 2006, 7:R16. 10.1186/gb-2006-7-2-r16, 1431731, 16507177.
14. Braumann I, van den Berg MA, Kempken F. Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain. Mol Genet Genom 2008, 280:319-325.
15. Panaccione DG, Pitkin JW, Walton JD, Annis SL. Transposon-like sequences at the TOX2 locus of the plant-pathogenic fungus Cochliobolus carbonum. Gene 1996, 176:103-109. 10.1016/0378-1119(96)00228-4, 8918240.
16. Hatta R, Ito K, Hosaki Y, Tanaka T, Tanaka A, Yamamoto M, Akimitsu K, Tsuge T. A conditionally dispensable chromosome controls host-specific pathogenicity in the fungal plant pathogen Alternaria alternata. Genetics 2002, 161:59-70. 1462115, 12019223.
17. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, Thon M, Kulkarni R, Xu J-R, Pan H, Read ND, Lee Y-H, Carbone I, Brown D, Oh YY, Donofrio N, Jeong JS, Soanes DM, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun M-H, Bohnert H, Coughlan S, Butler J, Calvo S, Ma L-J, Nicol R, Purcell S, Nusbaum C, Galagan JE, Birren BW. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 2005, 434:980-986. 10.1038/nature03449, 15846337.
18. Daboussi MJ, Capy P. Transposable elements in filamentous fungi. Annu Rev Microbiol 2003, 57:275-299. 10.1146/annurev.micro.57.030502.091029, 14527280.
19. Aravin AA, Hannon GJ, Brennecke J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 2007, 318:761-764. 10.1126/science.1146484, 17975059.
20. Lisch D. Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 2009, 60:43-66. 10.1146/annurev.arplant.59.032607.092744, 19007329.
21. Galagan JE, Selker EU. RIP: the evolutionary cost of genome defense. Trends Genet 2004, 20:417-423. 10.1016/j.tig.2004.07.007, 15313550.
22. Cambareri E, Jensen B, Schabtach E, Selker E. Repeat-induced G-C to A-T mutations in Neurospora. Science 1989, 244:1571-1575. 10.1126/science.2544994, 2544994.
23. Braumann I, Van den Berg M, Kempken F. Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum. Curr Genet 2008, 53:287-297. 10.1007/s00294-008-0185-y, 18347798.
24. Harrell L, Melcher U, Atkins JF. Predominance of six different hexanucleotide recoding signals 3' of read-through stop codons. Nucl Acids Res 2002, 30:2011-2017. 10.1093/nar/30.9.2011, 113845, 11972340.
25. Konieczny A, Voytas DF, Cummings MP, Ausubel FM. A superfamily of Arabidopsis thaliana retrotransposons. Genetics 1991, 127:801-809. 1204407, 1709409.
26. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 1998, 8:464-478.
27. Marin I, Llorens C. Ty3/Gypsy retrotransposons:description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol Biol Evol 2000, 17:1040-1049. 10.1093/oxfordjournals.molbev.a026385, 10889217.
28. Zhu P, Oudemans PV. A long terminal repeat retrotransposon Cgret from the phytopathogenic fungus Colletotrichum gloeosporioides on cranberry. Curr Genet 2000, 38:241-247. 10.1007/s002940000162, 11191207.
29. Bouvet GF, Jacobi V, Bernier L. Characterization of three DNA transposons in the Dutch elm disease fungi and evidence of repeat-induced point (RIP) mutations. Fungal Genet Biol 2007, 44:430-443. 10.1016/j.fgb.2006.11.016, 17291794.
30. Kempken F, Windhofer F. The hAT family: a versatile transposon group common to plants, fungi, animals, and man. Chromosoma 2001, 110:1-9. 10.1007/s004120000118, 11398971.
31. Linder-Basso D, Foglia R, Zhu P, Hillman BI. Crypt1, an active Ac-like transposon from the chestnut blight fungus, Cryphonectria parasitica. Mol Genet Genom 2001, 265:730-738.
32. Rep M, van der Does HC, Cornelissen BJC. Drifter, a novel, low copy hAT-like transposon in Fusarium oxysporum is activated during starvation. Fungal Genet Biol 2005, 42:546-553. 10.1016/j.fgb.2005.03.007, 15869889.
33. Okuda M, Ikeda K, Namiki F, Nishi K, Tsuge T. Tfo1: an Ac-like transposon from the plant pathogenic fungus Fusarium oxysporum. Mol Gen Genet 1998, 258:599-607. 10.1007/s004380050773, 9671028.
34. Kempken F, Kuck U. Restless, an active Ac-like transposon from the fungus Tolypocladium inflatum: Structure, expression, and alternative RNA splicing. Mol Cell Biol 1996, 16:6563-6572. 231658, 8887685.
35. Gao Q, Jin K, Ying S-H, Zhang Y, Xiao G, Shang Y, Duan Z, Hu X, Xie X-Q, Zhou G, Peng G, Luo Z, Huang W, Wang B, Fang W, Wang S, Zhong Y, Ma L-J, St Leger RJ, Zhao G-P, Pei Y, Feng M-G, Xia Y, Wang C. Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet 2011, 7:e1001264. 10.1371/journal.pgen.1001264, 3017113, 21253567.
36. Chalvet F, Grimaldi C, Kaper F, Langin T, Daboussi MJ. Hop, an active Mutator-like element in the genome of the fungus Fusarium oxysporum. Mol Biol Evol 2003, 20:1362-1375. 10.1093/molbev/msg155, 12777515.
37. Sokal RR, Rohlf FJ. Biometry, the principles and practice of statistics in biological research, analysis of frequencies 1995, W.H. Freeman and Company, New York, 3.
38. Ikeda K, Nakayashiki H, Takagi M, Tosa Y, Mayama S. Heat shock, copper sulfate and oxidative stress activate the retrotransposon MAGGY resident in the plant pathogenic fungus Magnaporthe grisea. Mol Genet Genom 2001, 266:318-325.
39. Ogasawara H, Obata H, Hata Y, Takahashi S, Gomi K. Crawler, a novel Tc1/mariner-type transposable element in Aspergillus oryzae transposes under stress conditions. Fungal Genet Biol 2009, 46:441-449. 10.1016/j.fgb.2009.02.007, 19269345.
40. Anava N, Roncero MIG. Skippy, a retrotransposon from the fungal plant pathogen Fusarium oxysporum. Mol Gen Genet 1995, 249:637-647. 10.1007/BF00418033, 8544829.
41. Levis C, Fortini D, Brygoo Y. Flipper, a mobile Fot1-like transposable element in Botrytis cinerea. Mol Gen Genet 1997, 254:674-680. 10.1007/s004380050465, 9202383.
42. Daboussi MJ, Langin T, Brygoo Y. Fot1, a new family of fungal transposable elements. Mol Gen Genet 1992, 232:12-16. 10.1007/BF00299131, 1313143.
43. Enkerli J, Bhatt G, Covert SF. Nht1, a transposable element cloned from a dispensable chromosome in Nectria haematococca. Mol Plant Microb Interac 1997, 10:742-749.
44. Hane J, Oliver R. RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. BMC Bioinforma 2008, 9:478.
45. Joaquim TR, Rowe RC. Reassessment of vegetative compatibility relationships among strains of Verticillium dahliae using nitrate-nonutilizing mutants. Phytopathology 1990, 80:1160-1166.
46. Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF. Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA 2003, 9:1422-1430. 10.1261/rna.5105503, 1370496, 14623998.
47. Forbes E, Nieduszynska S, Brunton F, Gibson J, Glover LA, Stansfield I. Control of gag-pol gene expression in the Candida albicans retrotransposon Tca2. BMC Mol Biol 2007, 8:94. 10.1186/1471-2199-8-94, 2194720, 17961216.
48. Lauermann V, Hermankova M, Boeke JD. Increased length of long terminal repeats inhibits Ty1 transposition and leads to the formation of tandem multimers. Genetics 1997, 145:911-922. 1207896, 9093846.
49. Brillet B, Benjamin B, Bigot Y, Yves B, Auge-Gouillou C, Corinne A-G. Assembly of the Tc1 and mariner transposition initiation complexes depends on the origins of their transposase DNA binding domains. Genetica 2007, 130:105-120. 10.1007/s10709-006-0025-2, 16912840.
50. Tudor M, Lobocka M, Goodell M, Pettitt J, Ohare K. The pogo transposable element family of Drosophila melanogaster. Mol Gen Genet 1992, 232:126-134. 10.1007/BF00299145, 1313144.
51. Hickman AB, Chandler M, Dyda F. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 2010, 45:50-69. 10.3109/10409230903505596, 3107681, 20067338.
52. Yuan YW, Wessler SR. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci USA 2011, 108:7884-7889. 10.1073/pnas.1104208108, 3093488, 21518873.
53. Vos JC, DeBaere I, Plasterk RHA. Transposase is the only nematode protein required for in vitro transposition of Tc1. Genes Dev 1996, 10:755-761. 10.1101/gad.10.6.755, 8598301.
54. Gueiros-Filho FJ, Beverley SM. Development of a heterologous transposon system for Leishmania. Memorias Instituto Oswaldo Cruz 1997, 92:16.
55. Fadool JM, Hartl DL, Dowling JE. Transposition of the mariner element from Drosophila mauritiana in zebrafish. Proc Natl Acad Sci USA 1998, 95:5182-5186. 10.1073/pnas.95.9.5182, 20235, 9560250.
56. Sherman A, Dawson A, Mather C, Gilhooley H, Li Y, Mitchell R, Finnegan D, Sang H. Transposition of the Drosophila element mariner into the chicken germ line. Nat Biotechnol 1998, 16:1050-1053. 10.1038/3497, 9831034.
57. Tosi LRO, Beverley SM. Cis and trans factors affecting Mos1 mariner evolution and transposition in vitro, and its potential for functional genomics. Nucl Acids Res 2000, 28:784-790. 10.1093/nar/28.3.784, 102556, 10637331.
58. Pledger DW, Fu YQ, Coates CJ. Analyses of cis-acting elements that affect the transposition of Mos1 mariner transposons in vivo. Mol Genet Genom 2004, 272:67-75.
59. Casteret S, Chbab N, Cambefort J, Auge-Gouillou C, Bigot Y, Rouleux-Bonnin F. Physical properties of DNA components affecting the transposition efficiency of the mariner Mos1 element. Mol Genet Genom 2009, 282:531-546.
60. Marini M, Zanforlin T, Santos P, Barros R, Guerra A, Puccia R, Felipe M, Brigido M, Soares C, Ruiz J, Silveira J, Cisalpino P. Identification and characterization of Tc1/mariner-like DNA transposons in genomes of the pathogenic fungi of the Paracoccidioides species complex. BMC Genomics 2010, 11:130. 10.1186/1471-2164-11-130, 2836289, 20178623.
61. Hua-Van A, Daviere J-M, Kaper F, Langin T, Daboussi M-J. Genome organization in Fusarium oxysporum: clusters of class II transposons. Curr Genet 2000, 37:339-347. 10.1007/s002940050537, 10853772.
62. Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucl Acids Res 2006, 34:e57. 10.1093/nar/gkl184, 1450332, 16648358.
63. Kondrychyn I, Garcia-Lecea M, Emelyanov A, Parinov S, Korzh V. Genome-wide analysis of Tol2 transposon reintegration in zebrafish. BMC Genomics 2009, 10:418. 10.1186/1471-2164-10-418, 2753552, 19737393.
64. Voytas DF, Boeke JD. Yeast retrotransposons and tRNAs. Trends Genet 1993, 9:421-427. 10.1016/0168-9525(93)90105-Q, 8122309.
65. Crouch JA, Glasheen BM, Giunta MA, Clarke BB, Hillman BI. The evolution of transposon repeat-induced point mutation in the genome of Colletotrichum cereale: Reconciling sex, recombination and homoplasy in an "asexual" pathogen. Fungal Genet Biol 2008, 45:190-206. 10.1016/j.fgb.2007.08.004, 17962053.
66. Montiel MD, Lee HA, Archer DB. Evidence of RIP (repeat-induced point mutation) in transposase sequences of Aspergillus oryzae. Fungal Genet Biol 2006, 43:439-445. 10.1016/j.fgb.2006.01.011, 16531081.
67. Freitag M, Williams RL, Kothe GO, Selker EU. A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Natl Acad Sci USA 2002, 99:8802-8807. 10.1073/pnas.132212899, 124379, 12072568.
68. Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie XH, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RAE, Chapman S, Coulson R, Coutinho PM, Danchin EGJ, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li LD, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng QD, Zhou SG, Galagan J, Cuomo CA, Kistler HC, Rep M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010, 464:367-373. 10.1038/nature08850, 3048781, 20237561.
69. Belyayev A, Kalendar R, Brodsky L, Nevo E, Schulman A, Raskina O. Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mob DNA 2010, 1:6. 10.1186/1759-8753-1-6, 2836003, 20226076.
70. Bennetzen JL, Ramakrishna W. Exceptional haplotype variation in maize. Proc Natl Acad Sci USA 2002, 99:9093-9095. 10.1073/pnas.152336699, 123097, 12093929.
71. Huang X, Lu G, Zhao Q, Liu X, Han B. Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol 2008, 148:25-40. 10.1104/pp.108.121491, 2528094, 18650402.
72. Picot S, Wallau GL, Loreto ELS, Heredia FO, Hua-Van A, Capy P. The mariner transposable element in natural populations of Drosophila simulans. Heredity 2008, 101:53-59. 10.1038/hdy.2008.27, 18461087.
73. Wright SI, Le QH, Schoen DJ, Bureau TE. Population dynamics of an Ac-like transposable element in self- and cross-pollinating Arabidopsis. Genetics 2001, 158:1279-1288. 1461736, 11454774.
74. Favarol LCL, AraujoII WL, AzevedoIII JL, Paccola-Meirelles LD. The biology and potential for genetic research of transposable elements in filamentous fungi. Genet Mol Biol 2005, 28:804-813.
75. Klosterman SJ, Atallah ZK, Vallad GE, Subbarao KV. Diversity, pathogenicity, and management of Verticillium species. Annu Rev Phytopathol 2009, 47:39-62. 10.1146/annurev-phyto-080508-081748, 19385730.
76. Atallah ZK, Maruthachalam K, du Toit L, Koike ST, Davis RM, Klosterman SJ, Hayes RJ, Subbarao KV. Population analyses of the vascular plant pathogen Verticillium dahliae detect recombination and transcontinental gene flow. Fungal Genet Biol 2010, 47:416-422. 10.1016/j.fgb.2010.02.003, 20149887.
77. Bhat RG, Subbarao KV. Host range specificity in Verticillium dahliae. Phytopathology 1999, 89:1218-1225. 10.1094/PHYTO.1999.89.12.1218, 18944648.
78. Qin QM, Vallad GE, Wu BM, Subbarao KV. Phylogenetic analyses of phytopathogenic isolates of Verticillium spp. Phytopathology 2006, 96:582-592. 10.1094/PHYTO-96-0582, 18943175.
79. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 1998, 8:175-185.
80. Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucl Acids Res 2004, 32:W327-W331. 10.1093/nar/gkh454, 441592, 15215404.
81. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH. CDD: specific functional annotation with the Conserved Domain Database. Nucl Acids Res 2009, 37:D205-D210. 10.1093/nar/gkn845, 2686570, 18984618.
82. Dobinson KF. Genetic transformation of the vascular wilt fungus Verticillium dahliae. Can J Bot 1995, 73:710-715.
83. Klimes A, Dobinson KF. A hydrophobin gene, VDH1, is involved in microsclerotial development and spore viability in the plant pathogen Verticillium dahliae. Fungal Genet Biol 2006, 43:283-294. 10.1016/j.fgb.2005.12.006, 16488633.
84. Edgar R. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma 2004, 5:113.