Evolutionary sequence analysis of complete eukaryote genomes

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Blair, Jaime E ^a   Shah, Prachi ^a   Hedges, S Blair ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLETE GENOMES; CONVENTIONAL METHODS; GENE DUPLICATIONS; GENOME COMPARISON; ORTHOLOGOUS GENES; POTENTIAL ERRORS; SEQUENCE ANALYSIS; SINGLE-COPY GENES;

AMINO ACIDS; BIOLOGY; COPOLYMERIZATION; ESTIMATION; PROTEINS;

GENES;

AMINO ACID SEQUENCE; ARTHROPOD; CONTROLLED STUDY; EUKARYOTE; EUKARYOTE EVOLUTION; FOSSIL; GENE DUPLICATION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CONSERVATION; NONHUMAN; PHYLOGENY; PRECAMBRIAN; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIVERSITY; ANIMAL; ARCHAEAL GENOME; BIODIVERSITY; BIOLOGICAL MODEL; BIOLOGY; COMPUTER LANGUAGE; COMPUTER PROGRAM; CYTOLOGY; DNA SEQUENCE; EUKARYOTIC CELL; EVOLUTION; GENETIC DATABASE; GENOME; HUMAN; MOLECULAR EVOLUTION; PROCEDURES; PROTEIN DATABASE; TIME;

ANIMALIA; ARTHROPODA; EUKARYOTA;

PROTEIN;

ANIMALS; BIODIVERSITY; BIOLOGICAL EVOLUTION; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; FOSSILS; GENE DUPLICATION; GENOME; GENOME, ARCHAEAL; HUMANS; MODELS, GENETIC; PHYLOGENY; PROGRAMMING LANGUAGES; PROTEINS; SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; TIME FACTORS;

EID: 22944471282     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-53     Document Type: Review

References (80)

1. Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV: Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evolutionary Biology 2001, 1:8.
2. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE: Whole-genome analysis of photosynthetic prokaryotes. Science 2002, 298:1616-1620.
3. Brochier C, Forterre P, Gribaldo S: Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biology 2004, 5:R17.
4. Korbel JO, Snel B, Huynen MA, Bork P: SHOT: a web server for the construction of genome phylogenies. Trends in Genetics 2002, 18:158-162.
5. House CH, Runnegar B, Fitz-Gibbon ST: Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and Eukarya. Geobiology 2003, 1:15-26.
6. Wolf YI, Rogozin IB, Koonin EV: Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Research 2004, 14:29-36.
7. Copley RR, Aloy P, Russell RB, Telford MJ: Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans. Evolution and Development 2004, 6:164-169.
8. Krylov DM, Wolf YI, Rogozin IB, Koonin EV: Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Research 2003, 13:2229-2235.
9. Hughes AL, Friedman R: Differential loss of ancestral gene families as a source of genomic divergence in animals. Proceedings of the Royal Society of London B: Biological Sciences 2004, 271:S107-109.
10. Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV: Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Current Biology 2003, 13:1512-1517.
11. Coghlan A, Wolfe KH: Origins of recently gained introns in Caenorhabditis. PNAS 2004, 101:11362-11367.
12. Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J: Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Research 2002, 12:493-502.
13. Li L, Stoeckert CJJ, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research 2003, 13:2178-2189.
14. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biology 2004, 5:R7.
15. Sonnhammer ELL, Koonin EV: Orthology, paralogy and proposed classification for paralog subtypes. Trends in Genetics 2002, 18:619-620.
16. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, et al.: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
17. Hedges SB, Blair JE, Venturi ML, Shoe JL: A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evolutionary Biology 2004, 4:2.
18. Blair JE, Ikeo K, Gojobori T, Hedges SB: The evolutionary position of nematodes. BMC Evolutionary Biology 2002, 2:7.
19. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, et al.: Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004, 428:493-521.
20. Coghlan A, Wolfe KH: Fourfold Faster Rate of Genome Rearrangement in Nematodes Than in Drosophila. Genome Res 2002, 12:857-867.
21. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH: The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics. PLoS Biology 2003, 1:E45.
22. Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P: Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 2002, 298:149-159.
23. Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu X, Reith M, Cavalier-Smith T, Maier UG: The highly reduced genome of an enslaved algal nucleus. Nature 2001, 410:1091-1096.
24. Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP: Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 2001, 414:450-453.
25. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DMA, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511.
26. Pizzi E, Frontali C: Low-Complexity Regions in Plasmodium falciparum Proteins. Genome Res 2001, 11:218-229.
27. Felsenstein J: Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 1978, 27:401-410.
28. Rokas A, Williams BL, King N, Carroll SB: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
29. Gadagkar SR, Rosenberg MS, Kumar S: Inferring species phylogenies from multiple genes: Concatenated seqeunce tree versus consensus gene tree. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 2005, 304B:64-74.
30. Wray GA, Levinton JS, Shapiro LH: Molecular evidence for deep Precambrian divergences among metazoan phyla. Science 1996, 274:568-573.
31. Feng DF, Cho G, Doolittle RF: Determining divergence times with a protein clock: update and reevaluation. Proc Nat Acad Sci U S A 1997, 94:13028-13033.
32. Wang DY, Kumar S, Hedges SB: Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proceedings of the Royal Society of London B: Biological Sciences 1999, 266:163-171.
33. Nei M, Xu P, Glazko G: Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc Natl Acad Sci U S A 2001, 98:2497-2502.
34. Hedges SB, Kumar S: Precision of molecular time estimates. Trends in Genetics 2004, 20:242-247.
35. Peterson KJ, Lyons JB, Nowak KS, Takacs CM, Wargo MJ, McPeek MA: Estimating metazoan divergence times with a molecular clock. Proc Natl Acad Sci U S A 2004, 101:6536-6541.
36. Douzery EJP, Snell EA, Bapteste E, Delsuc F, Philippe H: The timing of eukaryote evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci U S A 2004, 101:15386-15391.
37. Aris-Brosou S, Yang Z: Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Molecular Biology and Evolution 2003, 20:1947-1954.
38. Kumar S: Mesoproterozoic megafossil Chuaria-Tawuia association may represent parts of a multicellular plant, Vindhyan Supergroup, Central India. Precambrian Res 2001, 106:187-211.
39. Woods KN, Knoll AH, German TN: Xanthophyte Algae from the Mesoproterozoic/Neoproterozoic Transition: Confirmation and Evolutionary Implications. GSA Abstracts with Programs 1998, 30:A232.
40. Butterfield NJ: Bangiomorpha pubescens n. gen., n. sp.: Implications for the Evolution of Sex, Multicellularity, and the Mesoproterozoic/Neoproterozoic Radiation of Eukaryotes. Paleobiology 2000, 26:386-404.
41. Blair JE, Hedges SB: Molecular Clocks Do Not Support the Cambrian Explosion. Mol Biol Evol 2005, 22:387-390.
42. Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M: Inferring non-neutral evolution from human-chimp-mouse orthologous gene trios. Science 2003, 302:1960-1963.
43. Kumar S, Subramanian S: Mutation rates in mammalian genomes. Proc Natl Acad Sci U S A 2002, 99:803-808.
44. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
45. Remm M, Storm CE, Sonnhammer EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 2001, 314:1041-1052.
46. Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research 2000, 28:33-36.
47. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, et al.: The sequence of the human genome. Science 2001, 291:1304-1351.
48. Ensembl Genome Browser: http://www.ensembl.org/..
49. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, et al.: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
50. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MDS, 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 YJK, 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: Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes. Science 2002, 297:1301-1310.
51. DOE Joint Genome Institute: http://www.jgi.doe.gov/..
52. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS: The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 2002, 298:2157-2167.
53. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, et al.: The genome sequence of Drosophila melanogaster. Science 2000, 287:2185-2195.
54. Berkeley Drosophilia Genome Project [http://www.fruitfly.org]
55. Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, et al.: The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002, 298:129-149.
56. The C. elegans Sequencing Consortium: Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998, 282:2012-2018.
57. Wormbase: [http://www.wormbase.org]
58. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG: Life with 6000 genes. Science 1996, 274:546, 563-7.
59. Saccharomyces Genome Database [http://www.yeastgenome.org]
60. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B: The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003, 422:859-868.
61. Broad Institute [http://www.broad.mit.edu]
62. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P: The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 2004, 304:304-307.
63. Ashbya Genome Database [http://agd.unibas.ch]
64. European Bioinformatics Institute [http://www.ebi.ac.uk/]
65. The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
66. The Institute for Genomic Research [http://www.tigr.org/]
67. Matsuzaki M, Misumi O, Shin IT, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Yoshida Y, Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F, Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H, Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T: Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 2004, 428:653-657.
68. Cyanidioschyzon merolae Genome Project [http://merolae.biol.s.u-tokyo.ac.jp]
69. PlasmoDB: [http://www.plasmodb.org]
70. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 1997, 25:4876-4882.
71. Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 1997, 13:555-556.
72. Kumar S, Tamura K, Jakobsen I, Nei M: MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 2001, 17:1244-1245.
73. Strimmer K, von Haeseler A: Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies. Mol Biol Evol 1996, 13:964-969.
74. Felsenstein J: Phylip: Phylogeny Inference Package. 3.6(a3) edition. Seattle, Department of Genome Sciences, University of Washington; 2002.
75. Kishino H, Thorne JL, Bruno WJ: Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution 2001, 18:352-361.
76. Jacobs LL, Downs WR: The evolution of murine rodents in Asia. In Rodent and Lagomorph Families of Asian Origins and Diversification Volume 8. Edited by: Tomida Y, Li CK and Setoguchi T. Tokyo, National Science Museum Monographs; 1994:149-156.
77. Benton MJ: The Fossil Record 2. New York, Chapman & Hall; 1993.
78. Donoghue PCJ, Smith MP, Sansom IJ: The origin and early evolution of chordates: molecular clocks and the fossil record. In Telling the Evolutionary Time: Molecular Clocks and the Fossil Record Edited by: Donoghue PCJ and Smith MP. New York, CRC Press; 2004:190-223.
79. Shu DG, Chen L, Han J, Zhang XL: An Early Cambrian tunicate from China. Nature 2001, 411:472-473.
80. Gaunt MW, Miles MA: An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Molecular Biology and Evolution 2002, 19:748-761.