Resolving the question of trypanosome monophyly: A comparative genomics approach using whole genome data sets with low taxon sampling

Infection, Genetics and Evolution

Volumn 11, Issue 5, 2011, Pages 955-959

  Leonard, Guy ^a,b   Soanes, Darren M ^a   Stevens, Jamie R ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

Kinetoplastida; Leishmania; Monophyletic; Orthologue; Paralogous genes; Paralogue; Paraphyletic; Trypanosoma

Indexed keywords

ARTICLE; EUGLENA GRACILIS; GENETIC DATABASE; GENETIC MARKER; GENOME; GENOME ANALYSIS; GENOMICS; KINETOPLASTIDA; LEISHMANIA MAJOR; MONOPHYLY; MULTIGENE FAMILY; NAEGLERIA GRUBERI; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; TAXONOMY; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI;

GENOME, PROTOZOAN; GENOMICS; PHYLOGENY; TRYPANOSOMA;

EUGLENA GRACILIS; HEXAPODA; KINETOPLASTIDA; LEISHMANIA MAJOR; LEISHMANIA SP.; NAEGLERIA GRUBERI; TRYPANOSOMA; TRYPANOSOMA BRUCEI; TRYPANOSOMA CRUZI; TRYPANOSOMATIDAE; VERTEBRATA;

EID: 79956322945     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.03.005     Document Type: Article

References (49)

1. Adjé C.A., Opperdoes F.R., Michels P.A.M. Molecular analysis of phosphoglycerate kinase in Trypanoplasma borreli and the evolution of this enzyme in Kinetoplastida. Gene 1998, 217:91-99.
2. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
3. Alvarez F., Cortinas M.N., Musto H. The analysis of protein coding genes suggests monophyly of Trypanosoma. Mol. Phylogenet. Evol. 1996, 5:333-343.
4. Baker J.R. Speculations on the evolution of the family Trypanosomatidae Doflein 1901. Exp. Parasitol. 1963, 13:219-233.
5. Baker J.R. The origins of parasitism in the protists. Intl. J. Parasitol. 1994, 24:1131-1137.
6. Berriman M., Ghedin E., Hertz-Fowler C., Blandin G., Renauld H., Bartholomeu D.C., et al. The genome of the African trypanosome Trypanosoma brucei. Science 2005, 309:416-422.
7. Brown J.R., Doolittle W.F. Root of the universal tree of life based on ancient aminoacyl-transfer RNA synthetase gene duplications. Proc. Natl. Acad. Sci. U.S.A. 1995, 92:2441-2445.
8. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
9. Cavalier-Smith T. A revised six-kingdom system of life. Biol. Rev. Camb. Philos. Soc. 1998, 73:203-266.
10. Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113.
11. El-Sayed N.M., Myler P.J., Bartholomeu D.C., Nilsson D., Aggarwal G., Tran A.-N., et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 2005, 309:409-415.
12. Felsenstein J. Cases in which parsimony or compatibility will be positively misleading. Syst. Zool. 1978, 27:401-410.
13. Fritz-Laylin L.K., Prochnik S.E., Ginger M.L., Dacks J.B., Carpenter M.L., et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell 2010, 140:631-642.
14. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
15. Hampl V., Hug L., Leigh J.W., Dacks J.B., Lang B.F., et al. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic " supergroups" Proc. Natl. Acad. Sci. U.S.A. 2009, 106:3859-3864.
16. Hannaert V., Blaauw M., Kohl L., Allert S., Opperdoes F.R., Michels P.A. Molecular analysis of the cytosolic and glycosomal glyceraldehyde-3-phosphate dehydrogenase in Leishmania mexicana. Mol. Biochem. Parasitol. 1992, 55:115-126.
17. Hannaert V., Opperdoes F.R., Michels P.A.M. Comparison and evolutionary analysis of the glycosomal glyceraldehyde-3-phosphate dehydrogenase from different Kinetoplastida. J. Mol. Evol. 1998, 47:728-738.
18. Hashimoto T., Nakamura Y., Kamaishi T., Adachi J., Nakamura F., Okamoto K., Hasegawa M. Phylogenetic place of kinetoplastid protozoa inferred from a protein phylogeny of elongation factor 1α. Mol. Biochem. Parasitol. 1995, 70:181-185.
19. Hamilton P.B., Stevens J.R., Gaunt M.W., Gidley J., Gibson W.C. Trypanosomes are monophyletic: evidence from genes for glyceraldehyde phosphate dehydrogenase and small subunit ribosomal RNA. Intl. J. Parasitol. 2004, 34:1393-1404.
20. Hamilton P.B., Gibson W.C., Stevens J.R. Patterns of co-evolution between trypanosomes and their hosts deduced from ribosomal RNA and protein-coding gene phylogenies. Mol. Phylogen. Evol. 2007, 44:15-25.
21. Hamilton P.B., Stevens J.R. Classification and phylogeny of Trypanosoma cruzi. American Trypanosomiasis: Chagas Disease, One Hundred Years of Research 2010, 321-338. Elsevier, Chapter 13. J. Telleria, M. Tibayrenc (Eds.).
22. Hertz-Fowler C., Hall N. Parasite genome databases and web-based resources. Methods Mol. Biol. 2004, 270:45-74.
23. Hoare C.A. The Trypanosomes of Mammals 1972, Blackwell, Oxford, p. 749.
24. Huelsenbeck J.P., Ronquist F. MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
25. Hughes A.L., Piontkivska H. Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera. Mol. Biol. Evol. 2003, 20:644-652.
26. Ivens A.C., Peacock C.S., Worthey E.A., Murphy L., Aggarwal G., Berriman M., et al. The genome of the kinetoplastid parasite, Leishmania major. Science 2005, 309:436-442.
27. Keane T., Creevey C., Pentony M., Naughton T., McInerney J. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 2006, 6:29.
28. Lake J.A., de la Cruz V.F., Ferreira P.C., Morel C., Simpson L. Evolution of parasitism: kinetoplastid protozoan history reconstructed from mitochondrial rRNA gene sequences. Proc. Natl. Acad. Sci. U.S.A. 1988, 85:4779-4783.
29. Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
30. Le S.Q., Lartillot N., Gascuel O. Phylogenetic mixture models for proteins. Philos. Trans. R. Soc. B: Biol. Sci. 2008, 363:3965-3976.
31. Li L., Stoeckert C.J., Roos D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13:2178-2189.
32. Lukeš J., Jirků M., Doležel D., Kral'ová I., Hollar L., Maslov D.A. Analysis of ribosomal RNA genes suggests that trypanosomes are monophyletic. J. Mol. Evol. 1997, 44:521-527.
33. Maslov D.A., Lukes J., Jirku M., Simpson L. Phylogeny of trypanosomes as inferred from the small and large subunit rRNAs: implications for the evolution of parasitism in the trypanosomatid protozoa. Mol. Biochem. Parasitol. 1996, 75:197-205.
34. Minchin E.A. Investigations on the development of trypanosomes in tsetse flies and other Diptera. Q. J. Microsc. Sci. 1908, 52:159-260.
35. Molyneux D.H., Ashford R.W. The Biology of Trypanosoma and Leishmania, Parasites of Man and Domestic Animals 1983, Taylor and Francis, London, p. 294.
36. Pazos F., Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 2001, 14:609-614.
37. Philippe H., Zhou Y., Brinkmann H., Rodrigue N., Delsuc F. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 2005, 5:50.
38. Piontkivska H., Hughes A.L. Environmental kinetoplastid-like 18S rRNA sequences and phylogenetic relationships among Trypanosomatidae: paraphyly of the genus Trypanosoma. Mol. Biochem. Parasitol. 2005, 144:94-99.
39. Podlipaev S.A., Sturm N.R., Fiala I., Fernanades O., Westenberger S.J., Dollet M., Campbell D.A., Lukes J. Diversity of insect trypanosomatids assessed from the spliced leader RNA and 5S rRNA genes and intergenic regions. J. Eukaryot. Microbiol. 2004, 51:283-290.
40. Richards T.A., Soanes D.M., Foster P.G., Leonard G., Thornton C.R., Talbot N.J. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 2009, 21:1897-1911.
41. Simpson A.G., Lukes J., Roger A.J. The evolutionary history of kinetoplastids and their kinetoplasts. Mol. Biol. Evol. 2002, 19:2071-2083.
42. Simpson A.G.B., Gill E.E., Callahan H.A., Litaker R.W., Roger A.J. Early evolution within Kinetoplastids (Euglenozoa), and the late emergence of trypanosomatids. Protist 2004, 155:407-422.
43. Simpson A.G.B., Stevens J.R., Lukes J. The evolution and diversity of kinetoplastid flagellates. Trends Parasitol. 2006, 22:168-174.
44. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
45. Stevens J.R., Noyes H.A., Dover G.A., Gibson W.C. The ancient and divergent origins of the human pathogenic trypanosomes, Trypanosoma brucei and T. cruzi. Parasitology 1999, 118:107-116.
46. Stevens J.R., Noyes H.A., Schofield C.J., Gibson W. The molecular evolution of Trypanosomatidae. Adv. Parasitology 2001, 48:1-56.
47. TbestDB Taxonomically Broad EST Database 2010, http://amoebidia.bcm.umontreal.ca/pepdb/.
48. Wallace F.G. The trypanosomatid parasites of insects and arachnids. Exp. Parasitol. 1966, 18:124-193.
49. Wright A.-D.G., Li S., Feng S., Martin D.S., Lynn D.H. Phylogenetic position of the kinetoplastids, Cryptobia bullocki, Cryptobia catostomi, and Cryptobia salmositica and monophyly of the genus Trypanosoma inferred from small subunit ribosomal RNA sequences. Mol. Biochem. Parasitol. 1999, 99:69-76.