PhyloSift: Phylogenetic analysis of genomes and metagenomes

PeerJ

Volumn 2014, Issue 1, 2014, Pages

  Darling, Aaron E ^a,b   Jospin, Guillaume ^b   Lowe, Eric ^b   Matsen, Frederick A ^d   Bik, Holly M ^b   Eisen, Jonathan A ^b,c  

^a UNIVERSITY OF TECHNOLOGY SYDNEY   (Australia)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Bayes factor; Community structure; Edge PCA; Forensics; Metagenomics; Microbial diversity; Microbial ecology; Microbial evolution; Phylogenetic diversity; Phylogenetics

Indexed keywords

ARTICLE; BAYES THEOREM; DATA BASE; DNA SEQUENCE; HUMAN; METAGENOME; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PHYLOSIFT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TAXONOMY;

EID: 84895751645     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.243     Document Type: Article

References (68)

1. Abby SS, Tannier E, Gouy M, Daubin V. 2012. Lateral gene transfer as a support for the tree of life. Proceedings of the National Academy of Sciences of the United States of America DOI 10.1073/pnas.1116871109.
2. Adey A,Morrison H, Asan XX, Kitzman J, Turner E, Stackhouse B,MacKenzie A, Caruccio N, Zhang X, Shendure J. 2010. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biology 11(12):R119 DOI 10.1186/gb-2010-11-12-r119.
3. Altschul SF,Madden TL, Schöffer AA, Zhang J, Zhang Z,Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25(17):3389-3402 DOI 10.1093/nar/25.17.3389.
4. Béjá O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, DeLong EF. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289(5486):1902-1906 DOI 10.1126/science.289.5486.1902.
5. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK. 2012. Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology & Evolution 27(4):233-243 DOI 10.1016/j.tree.2011.11.010.
6. Blainey PC. 2013. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiology Reviews 37(3):407-427 DOI 10.1111/1574-6976.12015.
7. Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2012. Genome-scale coestimation of species and gene trees. Genome Research 23:323-330 DOI 10.1101/gr.141978.112.
8. Brady A, Salzberg SL. 2009. Phymm and phymmbl: metagenomic phylogenetic classification with interpolated markov models. Nature Methods 6(9):673-676 DOI 10.1038/nmeth.1358.
9. Brady A, Salzberg SL. 2011. Phymmbl expanded: confidence scores, custom databases, parallelization and more. Nature Methods 8(5):367 DOI 10.1038/nmeth0511-367.
10. Camacho C, Coulouris G, Avagyan V,Ma N, Papadopoulos J, Bealer K,Madden T. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10(1):421 DOI 10.1186/1471- 2105-10-421.
11. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA,McDonald D,Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, WaltersWA,Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7(5):335-336 DOI 10.1038/nmeth.f.303.
12. Chen K, Pachter L. 2005. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Computational Biology 1(2):e24 DOI 10.1371/journal.pcbi.0010024.
13. Diaz N, Krause L, Goesmann A, Niehaus K, Nattkemper T. 2009. TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics 10(1):56 DOI 10.1186/1471-2105-10-56.
14. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF. 2009. Community-wide analysis of microbial genome sequence signatures. Genome Biology 10(8):R85 DOI 10.1186/gb-2009-10-8-r85.
15. Eddy SR. 2011. Accelerated Profile HMM Searches. PLoS Computational Biology 7(10):e1002195 DOI 10.1371/journal.pcbi.1002195.
16. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research 8(3):163-167 DOI 10.1101/gr.8.3.163.
17. Eisen JA. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5(3):e82 DOI 10.1371/journal.pbio.0050082.
18. Eisen JA. 2012. Phylogenetic and phylogenomic approaches to analysis of microbial communities. In: The social biology of microbial communities - a report from the national academy of sciences forum on microbial threats. National Academy of Sciences, 180-212 DOI 10.6084/m9.figshare.841773.
19. Evans SN,Matsen FA. 2012. The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 74(3):569-592 DOI 10.1111/j.1467-9868.2011.01018.x.
20. Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61(1):1-10 DOI 10.1016/0006-3207(92)91201-3.
21. Ghosh TS,Mohammed MH, Komanduri D,Mande SS. 2011. Provide: a software tool for accurate estimation of viral diversity in metagenomic samples. Bioinformation 6(2):91-4 DOI 10.6026/97320630006091.
22. Gori F, Folino G, Jetten MSM,Marchiori E. 2011. MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. Bioinformatics 27(2):196-203 DOI 10.1093/bioinformatics/btq649.
23. Haque MM, Ghosh TS, Komanduri D,Mande SS. 2009. SOrt-ITEMS: sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics 25(14):1722-1730 DOI 10.1093/bioinformatics/btp317.
24. Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology 180(18):4765-4774.
25. Huson DH, Auch AF, Qi J, Schuster SC. 2007. MEGAN analysis of metagenomic data. Genome Research 17(3):377-386 DOI 10.1101/gr.5969107.
26. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM,Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ,Maiden MCJ. 2012. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158(Pt 4): 1005-1015 DOI 10.1099/mic.0.055459-0.
27. Kembel SW, Eisen JA, Pollard KS, Green JL. 2011. The phylogenetic diversity of metagenomes. PLoS ONE 6(8):e23214 DOI 10.1371/journal.pone.0023214.
28. Kielbasa SM,Wan R, Sato K, Horton P, Frith MC. 2011. Adaptive seeds tame genomic sequence comparison. Genome Research 21:487-493 DOI 10.1101/gr.113985.110.
29. Kunin V, Copeland A, Lapidus A,Mavromatis K, Hugenholtz P. 2008. A bioinformatician's guide to metagenomics. Microbiology and Molecular Biology Reviews 72(4):557-578 DOI 10.1128/MMBR.00009-08.
30. Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS ONE 8(4):e62510 DOI 10.1371/journal.pone.0062510.
31. Langmead B, Trapnell C, Pop M, Salzberg S. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3):R25 DOI 10.1186/gb-2009- 10-3-r25.
32. Lasken RS. 2012. Genomic sequencing of uncultured microorganisms from single cells. Nature Reviews Microbiology 10(9):631-640 DOI 10.1038/nrmicro2857.
33. Liu B, Gibbons T, Ghodsi M, Pop M. 2010. Metaphyler: taxonomic profiling for metagenomic sequences. In: 2010 IEEE international conference on bioinformatics and biomedicine (BIBM). IEEE, 95-100.
34. Löytynoja A, Vilella AJ, Goldman N. 2012. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28(13):1684-1691 DOI 10.1093/bioinformatics/bts198.
35. Lozupone C, Knight R. 2005. Unifrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71(12):8228-8235 DOI 10.1128/AEM.71.12.8228-8235.2005.
36. Matsen FA IV, Evans SN. 2013. Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. PLoS ONE 8:e56859 DOI 10.1371/journal.pone.0056859.
37. Matsen FA, Hoffman NG, Gallagher A, Stamatakis A. 2012. A format for phylogenetic placements. PLoS ONE 7(2):e31009 DOI 10.1371/journal.pone.0031009.
38. Matsen FA, Kodner RB, Armbrust EV. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11(1):538 DOI 10.1186/1471-2105-11-538.
39. McCoy CO,Matsen FA IV. 2013. Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth. PeerJ 1:e157 DOI 10.7717/peerj.157.
40. McHardy AC,Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I. 2006. Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods 4(1):63-72 DOI 10.1038/nmeth976.
41. Meyer F, Paarmann D, D'souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R,Wilke A,Wilkening J, Edwards RA. 2008. The metagenomics rast server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9(1):386 DOI 10.1186/1471-2105-9-386.
42. Miller C, Baker B, Thomas B, Singer S, Banfield J. 2011. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biology 12(5):R44 DOI 10.1186/gb-2011-12-5-r44.
43. Mohammed MH, Chadaram S, Komanduri D, Ghosh TS,Mande SS. 2011. Eu-detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets. Journal of Biosciences 36(4):709-717 DOI 10.1007/s12038-011-9105-2.
44. Morgan JL, Darling AE, Eisen JA. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5(4):e10209 DOI 10.1371/journal.pone.0010209.
45. Ondov B, Bergman N, Phillippy A. 2011. Interactive metagenomic visualization in aWeb browser. BMC Bioinformatics 12(1):385 DOI 10.1186/1471-2105-12-385.
46. Patil KR, Haider P, Pope PB, Turnbaugh PJ,Morrison M, Scheffer T,McHardy AC. 2011. Taxonomic metagenome sequence assignment with structured output models. Nature Methods 8:191-192 DOI 10.1038/nmeth0311-191.
47. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3):e9490 DOI 10.1371/journal.pone.0009490.
48. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, Darling A,Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, LiuW-T, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P,Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431-437 DOI 10.1038/nature12352.
49. Rosen GL, Reichenberger ER, Rosenfeld AM. 2011. NBC: the Nave Bayes Classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics 27(1):127-129 DOI 10.1093/bioinformatics/btq619.
50. Schloss PD,Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ,Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75(23):7537-7541 DOI 10.1128/AEM.01541-09.
51. Segata N,Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. 2012. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods 9(8):811-814 DOI 10.1038/nmeth.2066.
52. Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. 2011. Phylotu: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Computational Biology 7(1):e1001061 DOI 10.1371/journal.pcbi.1001061.
53. Shih PM,Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, De Marsac NT, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA,Woyke T, Gugger M, Kerfeld CA. 2013. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences of the United States of America 110(3):1053-1058 DOI 10.1073/pnas.1217107110.
54. Stark M, Berger S, Stamatakis A, Von Mering C. 2010. MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics 11(1):461 DOI 10.1186/1471-2164-11-461.
55. Sunagawa S,Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM,Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. 2013. Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods 10:1196-1199 DOI 10.1038/nmeth.2693.
56. Szãllåsi GJ, Boussau B, Abby SS, Tannier E, Daubin V. 2012. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proceedings of the National Academy of Sciences of the United States of America 109(43):17513-17518 DOI 10.1073/pnas.1202997109.
57. Thomas T, Gilbert J,Meyer F. 2012. Metagenomics - a guide from sampling to data analysis. Microbial Informatics and Experimentation 2:3 DOI 10.1186/2042-5783-2-3.
58. Tringe SG, VonMering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM. 2005. Comparative metagenomics of microbial communities. Science 308(5721):554-557 DOI 10.1126/science.1107851.
59. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428(6978):37-43 DOI 10.1038/nature02340.
60. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA,Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K,White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y-H, Smith HO. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667):66-74 DOI 10.1126/science.1093857.
61. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73(16):5261-5267 DOI 10.1128/AEM.00062-07.
62. Woyke T, Tighe D,Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A,Wu D, McCutcheon JP,McDonald BR,Moran NA, Bristow J, Cheng J-F. 2010. One bacterial cell, one complete genome. PLoS ONE 5(4):e10314 DOI 10.1371/journal.pone.0010314.
63. Wu D, Hugenholtz P,Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng J-F, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk H-P, Eisen JA. 2009. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462(7276):1056-1060 DOI 10.1038/nature08656.
64. Wu D, Jospin G, Eisen JA. 2013. Systematic identification of gene families for use as markers for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS ONE 8(10):e77033 DOI 10.1371/journal.pone.0077033.
65. Wu M, Scott AJ. 2012. Phylogenomic analysis of bacterial and archaeal sequences with amphora2. Bioinformatics 28(7):1033-1034 DOI 10.1093/bioinformatics/bts079.
66. Wu M, Eisen J. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9(10):R151 DOI 10.1186/gb-2008-9-10-r151.
67. Yatsunenko T, Rey FE,Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M,Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC,Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. 2012. Human gut microbiome viewed across age and geography. Nature 486:222-227 DOI 10.1038/nature11053.
68. Zhao Y, Tang H, Ye Y. 2011. RAPSearch2: a fast and memory-efficient protein similarity search tool for next generation sequencing data. Bioinformatics 28(1):125-126 DOI 10.1093/bioinformatics/btr595.