POTION: An end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Hongo, Jorge A ^a   de Castro, Giovanni M ^a   Cintra, Leandro C ^a   Zerlotini, Adhemar ^a   Lobo, Francisco P ^a  

^a EMBRAPA CERRADOS   (Brazil)

Author keywords

Comparative genomics; Genome scale positive selection detection; Molecular Darwinian positive selection

Indexed keywords

ARTICLE; AUTOMATION; BACTERIAL STRAIN; BIOINFORMATICS; CASE STUDY; COMPUTER PROGRAM; CONSERVATION GENETICS; CONTROLLED STUDY; GENE SEQUENCE; GENETIC DATABASE; GENETIC SELECTION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGENY; POSITIVE DARWINIAN SELECTION DETECTION; SEQUENCE HOMOLOGY; TRYPANOSOMA BRUCEI; BIOLOGY; GENETICS; HUMAN; HUMAN GENOME; MOLECULAR EVOLUTION; OPEN READING FRAME;

MYCOBACTERIUM TUBERCULOSIS; TRYPANOSOMA BRUCEI;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; OPEN READING FRAMES; PHYLOGENY; SELECTION, GENETIC; SEQUENCE HOMOLOGY;

EID: 84938077039     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1765-0     Document Type: Article

References (73)

1. Alfoldi J, Lindblad-Toh K. Comparative genomics as a tool to understand evolution and disease. Genome Res. 2013;23(7):1063-8.
2. Metzker ML. Sequencing technologies-the next generation. Nature reviews. 2010;11(1):31-46.
3. Lobo FP, Rodrigues MR, Rodrigues GO, Hilario HO, Souza RA, Tauch A, et al. KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa. Nucleic Acids Res. 2012;40(W1):W491-7.
4. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586-91.
5. Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 2000;15(12):496-503.
6. Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, et al. Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet. 2009;5(12), e1000753.
7. Kapralov MV, Filatov DA. Widespread positive selection in the photosynthetic Rubisco enzyme. BMC Evol Biol. 2007;7:73.
8. Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, et al. Patterns of positive selection in six Mammalian genomes. PLoS Genet. 2008;4(8):e1000144.
9. Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L. Patterns of positive selection in seven ant genomes. Mol Biol Evol. 2014;31(7):1661-85.
10. Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. Genome Res. 2007;17(9):1336-43.
11. Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, et al. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A. 2006;103(15):5977-82.
12. Soyer Y, Orsi RH, Rodriguez-Rivera LD, Sun Q, Wiedmann M. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evol Biol. 2009;9:264.
13. Suzuki H, Lefebure T, Bitar PP, Stanhope MJ. Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. BMC Genomics. 2012;13:38.
14. Lefebure T, Stanhope MJ. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 2007;8(5):R71.
15. Emes RD, Yang Z. Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLoS One. 2008;3(5):e2295.
16. Lefebure T, Stanhope MJ. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 2009;19(7):1224-32.
17. Moretti S, Murri R, Maffioletti S, Kuzniar A, Castella B, Salamin N, et al. gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution. Stud Health Technol Inform. 2012;175:59-68.
18. Markova-Raina P, Petrov D. High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Genome Res. 2011;21(6):863-74.
19. Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol Evol. 2009;1:114-8.
20. Anisimova M, Nielsen R, Yang Z. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics. 2003;164(3):1229-36.
21. Koonin EV. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 2005;39:309-38.
22. Anisimova M, Yang Z. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol. 2007;24(5):1219-28.
23. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12(10):1611-8.
24. Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics. 2006;172(4):2665-81.
25. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003;100(16):9440-5.
26. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Statist. 2001;29(4):1165-88.
27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7.
28. Loytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A. 2005;102(30):10557-62.
29. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772-80.
30. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972-3.
31. Retief JD. Phylogenetic analysis using PHYLIP. Methods Mol Biol. 2000;132:243-58.
32. El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, et al. Comparative genomics of trypanosomatid parasitic protozoa. Science (New York, NY). 2005;309(5733):404-9.
33. Xu Z, Chen H, Zhou R. Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae. BMC Evol Biol. 2011;11:203.
34. Liu X, Gutacker MM, Musser JM, Fu YX. Evidence for recombination in Mycobacterium tuberculosis. J Bacteriol. 2006;188(23):8169-77.
35. Anisimova M, Bielawski JP, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol. 2001;18(8):1585-92.
36. Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. PLoS Genet. 2008;4(12), e1000304.
37. Orsi RH, Sun Q, Wiedmann M. Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes. BMC Evol Biol. 2008;8:233.
38. Anisimova M, Bielawski J, Dunn K, Yang Z. Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol. 2007;7:154.
39. Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30(7):1575-84.
40. Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. 2002;Chapter 2:Unit 2 3.
41. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-10.
42. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000;302(1):205-17.
43. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 1997;14(7):685-95.
44. Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol. 2009;537:113-37.
45. Lew JM, Kapopoulou A, Jones LM, Cole ST. TubercuList-10 years after. Tuberculosis (Edinb). 2011;91(1):1-7.
46. Fritz C, Maass S, Kreft A, Bange FC. Dependence of Mycobacterium bovis BCG on anaerobic nitrate reductase for persistence is tissue specific. Infect Immun. 2002;70(1):286-91.
47. Houghton J, Townsend C, Williams AR, Rodgers A, Rand L, Walker KB, et al. Important role for Mycobacterium tuberculosis UvrD1 in pathogenesis and persistence apart from its function in nucleotide excision repair. J Bacteriol. 2012;194(11):2916-23.
48. Espitia C, Laclette JP, Mondragon-Palomino M, Amador A, Campuzano J, Martens A, et al. The PE-PGRS glycine-rich proteins of Mycobacterium tuberculosis: a new family of fibronectin-binding proteins? Microbiology. 1999;145(Pt 12):3487-95.
49. Namouchi A, Karboul A, Fabre M, Gutierrez MC, Mardassi H. Evolution of smooth tubercle Bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection. PLoS One. 2013;8(5), e64718.
50. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393(6685):537-44.
51. Sampson SL. Mycobacterial PE/PPE proteins at the host-pathogen interface. Clin Dev Immunol. 2011;2011:497203.
52. Zhang Y, Zhang H, Zhou T, Zhong Y, Jin Q. Genes under positive selection in Mycobacterium tuberculosis. Comput Biol Chem. 2011;35(5):319-22.
53. Chatterjee D, Khoo KH. Mycobacterial lipoarabinomannan: an extraordinary lipoheteroglycan with profound physiological effects. Glycobiology. 1998;8(2):113-20.
54. David R. The two faces of MycP1. Nat Rev Microbiol. 2010;8(5):314.
55. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005;21(16):3448-9.
56. Gotz S, Arnold R, Sebastian-Leon P, Martin-Rodriguez S, Tischler P, Jehl MA, et al. B2G-FAR, a species-centered GO annotation repository. Bioinformatics. 2011;27(7):919-24.
57. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002;18(3):502-4.
58. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312-3.
59. Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC. IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics. 2008;9:524.
60. Steinway SN, Dannenfelser R, Laucius CD, Hayes JE, Nayak S. JCoDA: a tool for detecting evolutionary selection. BMC Bioinformatics. 2010;11:284.
61. Delport W, Poon AF, Frost SD, Kosakovsky Pond SL. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics. 2010;26(19):2455-7.
62. Busset J, Cabau C, Meslin C, Pascal G. PhyleasProg: a user-oriented web server for wide evolutionary analyses. Nucleic Acids Res. 2011;39(Web Server issue):W479-85.
63. Stern A, Doron-Faigenboim A, Erez E, Martz E, Bacharach E, Pupko T. Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res. 2007;35(Web Server issue):W506-11.
64. Su F, Ou HY, Tao F, Tang H, Xu P. PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes. BMC Genomics. 2013;14:924.
65. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17(4):540-52.
66. Pond SL, Frost SD, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005;21(5):676-9.
67. Doron-Faigenboim A, Pupko T. A combined empirical and mechanistic codon model. Mol Biol Evol. 2007;24(2):388-97.
68. Sawyer S. Statistical tests for detecting gene conversion. Mol Biol Evol. 1989;6(5):526-38.
69. Gouveia-Oliveira R, Sackett PW, Pedersen AG. MaxAlign: maximizing usable data in an alignment. BMC Bioinformatics. 2007;8:312.
70. Gil M, Zanetti MS, Zoller S, Anisimova M. CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. Mol Biol Evol. 2013;30(6):1270-80.
71. Tanabe M, Kanehisa M. Using the KEGG database resource. Curr Protoc Bioinformatics. 2012;Chapter 1:Unit 1 12.
72. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25-9.
73. Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, et al. Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Res. 2014;42(Database issue):D917-21.