A phylogenomics approach for selecting robust sets of phylogenetic markers

Nucleic Acids Research

Volumn 42, Issue 7, 2014, Pages

  Capella Gutierrez, Salvador ^a,b   Kauff, Frank ^c   Gabaldón, Toni ^a,b,d  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c University of Koblenz Landau   (Germany)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASCOMYCETES; CLADISTICS; CYANOBACTERIUM; GENE SEQUENCE; MARKER GENE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENOMICS; PHYLOGENY; PRIORITY JOURNAL;

ASCOMYCOTA; CYANOBACTERIA; GENES, BACTERIAL; GENES, FUNGAL; GENETIC MARKERS; GENOMICS; PHYLOGENY;

EID: 84898949945     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku071     Document Type: Article

References (41)

1. Gurtler, V. and Mayall, B.C. (2001) Genomic approaches to typing, taxonomy and evolution of bacterial isolates. Int. J. Syst. Evol. Microbiol., 51, 3-16. (Pubitemid 32118404)
2. Delsuc, F., Brinkmann, H. and Philippe, H. (2005) Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet., 6, 361-375. (Pubitemid 40577180)
3. Leigh, J.W., Susko, E., Baumgartner, M. and Roger, A.J. (2008) Testing congruence in phylogenomic analysis. Syst. Biol., 57, 104-115.
4. Lerat, E., Daubin, V., Ochman, H. and Moran, N.A. (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol., 3, e130.
5. Susko, E., Leigh, J., Doolittle, W.F. and Bapteste, E. (2006) Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria. Mol. Biol. Evol., 23, 1019-1030. (Pubitemid 43726067)
6. Bayzid, M.S. and Warnow, T. (2013) Naive binning improves phylogenomic analyses. Bioinformatics, 29, 2277-2284.
7. Aguileta, G., Marthey, S., Chiapello, H., Lebrun, M.-H., Rodolphe, F., Fournier, E., Gendrault-Jacquemard, A. and Giraud, T. (2008) Assessing the performance of single-copy genes for recovering robust phylogenies. Syst. Biol., 57, 613-627.
8. Walker, D.M., Castlebury, L.A., Rossman, A.Y. and White, J.F. (2012) New molecular markers for fungal phylogenetics: two genes for species-level systematics in the Sordariomycetes (Ascomycota). Mol. Phylogenet. Evol., 64, 500-512.
9. Townsend, J.P. (2007) Profiling phylogenetic informativeness. Syst. Biol., 56, 222-231.
10. Salichos, L. and Rokas, A. (2013) Inferring ancient divergences requires genes with strong phylogenetic signals. Nature, 497, 327-331.
11. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
12. Huerta-Cepas, J., Capella-Gutierrez, S., Pryszcz, L.P., Denisov, I., Kormes, D., Marcet-Houben, M. and Gabaldon, T. (2011) PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res., 39, D556-D560.
13. Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
14. Katoh, K. and Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform., 9, 286-298. (Pubitemid 351890825)
15. Subramanian, A.R., Kaufmann, M. and Morgenstern, B. (2008) DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol. Biol., 3, 6.
16. Landan, G. and Graur, D. (2007) Heads or tails: a simple reliability check for multiple sequence alignments. Mol. Biol. Evol., 24, 1380-1383. (Pubitemid 47343943)
17. Wallace, I.M., O'Sullivan, O., Higgins, D.G. and Notredame, C. (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34, 1692-1699.
18. Capella-Gutierrez, S., Silla-Martinez, J.M. and Gabaldon, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.
19. Gascuel, O. (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol., 14, 685-695. (Pubitemid 27287289)
20. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.
21. Akaike, H.A. (1973) Information theory and an extension of the maximum likelihood principle. 2nd International Symposium on Information Theory.
22. Robinson, D.F. and Foulds, L.R. (1981) Comparison of phylogenetic trees. Math. Biosci., 53, 131-147. (Pubitemid 11129084)
23. Soria-Carrasco, V., Talavera, G., Igea, J. and Castresana, J. (2007) The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics, 23, 2954-2956. (Pubitemid 350162906)
24. Puigbo, P., Garcia-Vallve, S. and McInerney, J.O. (2007) TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics, 23, 1556-1558. (Pubitemid 47244483)
25. Huelsenbeck, J.P. and Bull, J.J. (1996) A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol., 45, 92-98.
26. Schopf, J. (2002) The fossil record: tracing the roots of the cyanobacterial lineage. In: Whitton, B.A. and Potts, M. (eds), The Ecology of Cyanobacteria. Kluwer Academic Publishers, Dordrecht, pp. 13-35.
27. Giovannoni, S.J., Turner, S., Olsen, G.J., Barns, S., Lane, D.J. and Pace, N.R. (1988) Evolutionary relationships among cyanobacteria and green chloroplasts. J. Bacteriol., 170, 3584-3592.
28. Seo, P.-S. and Yokota, A. (2003) The phylogenetic relationships of cyanobacteria inferred from 16S rRNA, gyrB, rpoC1 and rpoD1 gene sequences. J. Gen. Appl. Microbiol., 49, 191-203. (Pubitemid 37160913)
29. Henson, B.J., Watson, L.E. and Barnum, S.R. (2004) The evolutionary history of nitrogen fixation, as assessed by NifD. J. Mol. Evol., 58, 390-399. (Pubitemid 38501413)
30. Kauff, F. and Budel, B. (2011) Phylogeny of cyanobacteria: an overview. In: Luttge, U.E., Beyschlag, W., Budel, B., Francis, D. and Luttge, U. (eds), Progress in Botany, Vol. 72. Berlin Heidelberg, Springer, pp. 209-224.
31. Swingley, W.D., Blankenship, R. E. and Raymond, J. Insights into cyanobacterial evolution from comparative genomics, p. 21-43. In A. Herrero and E. Flores (ed.), The cyanobacteria: molecular biology, genomics and evolution, in press. Caister Academic Press, Norfolk, United Kingdom.
32. Shih, P.M., Wu, D., Latifi, A., Axen, S.D., Fewer, D.P., Talla, E., Calteau, A., Cai, F., Tandeau de Marsac, N., Rippka, R. et al. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc. Natl Acad. Sci. USA, 110, 1053-1058.
33. Hawksworth, D.L. (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol. Res., 105, 1422-1432. (Pubitemid 34134581)
34. Lutzoni, F., Kauff, F., Cox, C.J., McLaughlin, D., Celio, G., Dentinger, B., Padamsee, M., Hibbett, D., James, T.Y., Baloch, E. et al. (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am. J. Bot., 91, 1446-1480. (Pubitemid 43193713)
35. James, T.Y., Kauff, F., Schoch, C.L., Matheny, P.B., Hofstetter, V., Cox, C.J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J. et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature, 443, 818-822. (Pubitemid 44622687)
36. Marcet-Houben, M. and Gabaldon, T. (2009) The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PLoS One, 4, e4357.
37. Wang, H., Xu, Z., Gao, L. and Hao, B. (2009) A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol. Biol., 9, 195.
38. Ebersberger, I., de Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K. and von Haeseler, A. (2012) A consistent phylogenetic backbone for the fungi. Mol. Biol. Evol., 29, 1319-1334.
39. Capella-Gutierrez, S., Marcet-Houben, M. and Gabaldon, T. (2012) Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. BMC Biol., 10, 47.
40. Schoch, C.L., Sung, G.-H., Lopez-Giraldez, F., Townsend, J.P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P.B., Kauff, F., Wang, Z. et al. (2009) The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst. Biol., 58, 224-239.
41. Wang, Z. and Wu, M. (2013) A phylum-level bacterial phylogenetic marker database. Mol. Biol. Evol., 30, 1258-1262.