Comparing the dictyostelium and entamoeba genomes reveals an ancient split in the conosa lineage

PLoS Computational Biology

Volumn 1, Issue 7, 2005, Pages 0579-0584

  Song, Jie ^a   Xu, Qikai ^a   Olsen, Rolf ^a   Loomis, William F ^b   Shaulsky, Gad ^a   Kuspa, Adam ^a,b   Sucgang, Richard ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALS; DISEASE CONTROL; GENOME; PROTOZOA; TRANSCRIPTION;

CLASSIFIEDS; DICTYOSTELIUM; DICTYOSTELIUM DISCOIDEUM; ENTAMOEBA HISTOLYTICA; EUKARYOTIC GENOME; GENE FAMILIES; GENOMICS; ORTHOLOGOUS GENES; PHYLOGENETIC TREES; PUTATIVE TRANSCRIPTION FACTORS;

FUNGI;

PROTEOME; PROTOZOAL PROTEIN;

ANIMAL; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; DICTYOSTELIUM; ENTAMOEBA; GENE; GENETICS; GENOME; HUMAN; MULTIGENE FAMILY; PHYLOGENY; TIME;

ANIMALS; DICTYOSTELIUM; ENTAMOEBA; GENES, PROTOZOAN; GENOME, PROTOZOAN; HUMANS; MULTIGENE FAMILY; PHYLOGENY; PROTEOME; PROTOZOAN PROTEINS; TIME FACTORS;

EID: 55449127786     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010071.eor     Document Type: Article

References (23)

1. Miller W, Makova KD, Nekrutenko A, Hardison RC (2004) Comparative genomics. Annu Rev Genomics Hum Genet 5: 15-56.
2. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, et al. (2004) Genome evolution in yeasts. Nature 430: 35-44.
3. Kulathinal RJ, Hartl DL (2005) The latest buzz in comparative genomics. Genome Biol 6: 201.
4. Baldauf SL (2003) The deep roots of eukaryotes. Science 300: 1703-1706.
5. Eichinger L, Noegel A (2005) Comparative genomics of Dictyostelium discoideum and Entamoeba histolytica. Curr Opin Microbiol 8: 1-6.
6. EichingerL,Pachebat J A, Glockner G,RajandreamMA, SucgangR, et al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435: 43-57.
7. Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, et al. (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433: 865-868.
8. Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, et al. (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A 99: 1414-1419.
9. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4: 41.
10. Sipiczki M (2000) Where does fission yeast sit on the tree of life? Genome Biol 1: REVIEWS1011.
11. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-880.
12. Enright AJ, Kunin V, Ouzounis CA (2003) Protein families and TRIBES in genome sequence space. Nucleic Acids Res 31: 4632-4638.
13. Kobe B, Kajava AV (2001) The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 11: 725-732.
14. Raoult D, Audic S, Robert C, Abergel C, Renesto P, et al. (2004) The 1.2- megabase genome sequence of Mimivirus. Science 306: 1344-1350.
15. Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, et al. (2004) dictyBase: A new Dictyostelium discoideum genome database. Nucleic Acids Res 32: D332-D333.
16. Xu Q, Shaulsky G (2005) GOAT: An R tool for analyzing Gene Ontology term enrichment. Appl Bioinformatics 4: 281-283.
17. Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, et al. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 37: 283-328.
18. Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
19. Aspegren A, Hinas A, Larsson P, Larsson A, Söderbom F (2004) Novel noncoding RNAs in Dictyostelium discoideum and their expression during development. Nucleic Acids Res 32: 4646-4656.
20. Fukuzawa M, Hopper N, Williams J (1997) cudA: A Dictyostelium gene with pleiotropic effects on cellular differentiation and slug behaviour. Development 124: 2719-2728.
21. Clark CG, Diamond LS (2002) Methods for cultivation of luminal parasitic protists of clinical importance. Clin Microbiol Rev 15: 329-341.
22. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
23. Olsen RM, Loomis WF (2005) A collection of amino acid replacement matrices derived from clusters of orthologs. J Mol Evol 61: 659-665