An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Fan, Huan ^a,b,c   Ives, Anthony R ^c   Surget Groba, Yann ^d   Cannon, Charles H ^a,e  

^a KEY LABORATORY OF TROPICAL FOREST ECOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d UNIVERSITÉ DU QUÉBEC EN OUTAOUAIS   (Canada)

^e TEXAS TECH UNIVERSITY   (United States)

Author keywords

Alignment free; Assembly free; Homoplasy; k mers; Phylogenomics

Indexed keywords

ACCURACY; ARTICLE; ASSEMBLY AND ALIGNMENT FREE PHYLOGENETIC RECONSTRUCTION; BOOTSTRAPPING; GENETIC DISTANCE; GENETIC PROCEDURES; GENOME; GENOME SIZE; HOMOPLASY; HUMAN; INCOMPLETE SEQUENCING COVERAGE; K MER FILTERING; K MER LENGTH; MATHEMATICAL ANALYSIS; MATHEMATICAL PARAMETERS; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; SAMPLING; SEQUENCING ERROR; TIP CORRECTION; TREE; ALGORITHM; ANIMAL; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MAMMAL; NUCLEOTIDE SEQUENCE; PROCEDURES;

MAMMALIA;

ALGORITHMS; ANIMALS; BASE SEQUENCE; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MAMMALS; PHYLOGENY;

EID: 84938907619     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1647-5     Document Type: Article

References (50)

1. Felsenstein J: Inferring Phylogenies. Sinauer Associates Inc., Sunderland, MA 2004.
2. Straub SCK, Parks M, Weitemier K, Fishbein M, Cronn RC, Liston A. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. Am J Bot. 2012;99:349-64.
3. Garland Jr T, Harvey PH, IVES AR. Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts. Systematic Biol. 1992;41:18-32.
4. Yang Z, Rannala B: Molecular phylogenetics: principles and practice. Nature. Reviews Genetics. 2012;13:303-14.
5. Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005;6:361-75.
6. BOORE J. The use of genome-level characters for phylogenetic reconstruction. Trends Ecol Evol. 2006;21:439-46.
7. Ogden TH, Rosenberg MS. Multiple Sequence Alignment Accuracy and Phylogenetic Inference. Systematic Biol. 2006;55:314-28.
8. Chan CX, Ragan MA: Next-generation phylogenomics. Biology. Direct 2013;8:3.
9. Blaisdell BE. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc Natl Acad Sci. 1986;83:5155-9.
10. Dai Q, Yang Y, Wang T. Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. Bioinformatics. 2008;24:2296-302.
11. Yang K, Zhang L. Performance. comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Res. 2008;36:e33-3.
12. Lippert RA, Huang H, Waterman MS. Distributional regimes for the number of k-word matches between two random sequences. Proc Natl Acad Sci. 2002;99:13980-9.
13. Reinert G, Chew D, Sun F, Waterman MS. Alignment-Free Sequence Comparison (I): Statistics and Power. J Comput Biol. 2009;16:1615-34.
14. Domazet-Loso M, Haubold B. Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics. 2011;27:1466-72.
15. Qi J, Luo H, Hao BL. CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res. 2004;32:W45-7.
16. Stuart GW, Moffett K, Leader JJ. A Comprehensive Vertebrate Phylogeny Using Vector Representations of Protein Sequences from Whole Genomes. Mol Biol Evol. 2002;19:554-62.
17. Haubold B. Alignment-free phylogenetics and population genetics. Brief Bioinform. 2014;15:407-18.
18. Ulitsky I, Burstein D, Tuller T, Chor B. The Average Common Substring Approach to Phylogenomic Reconstruction. J Comput Biol. 2006;13:336-50.
19. Sims GE, Jun S-R, Wu GA, Kim S-H. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci. 2009;106:2677-82.
20. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Giga Science. 2012;1:18.
21. Li R, Fan W, Tian G, Zhu H, He L, Cai J, et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010;463:311-7.
22. Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, et al. Genome sequence and analysis of the tuber crop potato. Nature. 2011;475:189-95.
23. Baker M. De novo genome assembly: what every biologist should know. Nat Methods. 2012;9:333-7.
24. Cannon CH, C-S KUA, ZHANG D, HARTING JR. Assembly free comparative genomics of short-read sequence data discovers the needles in the haystack. Mol Ecol. 2010;19:147-61.
25. C-S KUA, Ruan J, Harting J, Ye C-X, Helmus MR, Yu J, et al. Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One. 2012;7:e48995.
26. Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F. Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads. J Comput Biol. 2013;20:64-79.
27. Roychowdhury T, Vishnoi A, Bhattacharya A. Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data. Sci Rep. 2013;3.
28. Maurer-Stroh S, Gunalan V, Wong W-c, Eisenhaber F. A Simple Shortcut To Unsupervised Alignment-free Phylogenetic Genome Groupings Even From Unassembled Sequencing Reads. J Bioinform Comput Biol. 2013;11:1343005.
29. Yi H, Jin L. Co-phylog:. an assembly-free phylogenomic approach for closely related organisms. Nucleic Acids Res. 2013;41:e75-5.
30. Prasad AB, Allard MW, NISC Comparative Sequencing Program, Green ED. Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets. Mol Biol Evol. 2008;25:1795-808.
31. Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MAM, et al. A Molecular Phylogeny of Living Primates. PLoS Genet. 2011;7:e1001342.
32. Kuhner MK, Felsenstein J. Simulation Comparison Of Phylogeny Algorithms Under Equal And Unequal Evolutionary Rates. Mol Biol Evol. 1994;11:459-68.
33. Meredith RW, Janecka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, et al. Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification. Science. 2011;334:521-4.
34. Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011;478:476-81.
35. Group AP. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical J Linnean Soc. 2009;161:105-21.
36. Oh S-H, Manos PS. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear. Taxon. 2008;57:434-51.
37. Manos PS, Cannon CH, Oh S-H. Phylogenetic Relationships and Taxonomic Status Of the Paleoendemic Fagaceae Of Western North America: Recognition Of A New Genus, Notholithocarpus. Madroño. 2008;55:181-90.
38. XU L, HARRISON RD, YANG P, YANG D-R. New insight into the phylogenetic and biogeographic history of genus Ficus: Vicariance played a relatively minor role compared with ecological opportunity and dispersal. Journal of Systematics and Evolution. 2011;49:546-57.
39. Cruaud A, Ronsted N, Chantarasuwan B, Chou LS, Clement WL, Couloux A, et al. An Extreme Case of Plant-Insect Codiversification: Figs and Fig-Pollinating Wasps. Systematic Biol. 2012;61:1029-47.
40. Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads. Mol Biol Evol. 2014;31:1077-88.
41. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20:265-72.
42. Nordström KJV, Albani MC, James GV, Gutjahr C, Hartwig B, Turck F, Paszkowski U, Coupland G, from mutant and wild-type individuals using k-mers. Nature Biotechnology 2013, 31:325-330.
43. Sanderson M, Boss D, Chen D, Cranston K, Wehe A. The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research. Systematic Biol. 2008;57:335-46.
44. Jukes TH, Cantor CR. Evolution of Protein Molecules. Volume 3. New York: Mammalian Protein Metabolism; 1969. p. 21-132.
45. Felsenstein J, PHYLIP. (Phylogeny Inference Package) version 3.6. 2005.
46. Kunsch HR. The Jackknife And The Bootstrap For General Stationary Observations. Annals of statistics. 1989;17:1217-41.
47. Hall P, Horowitz JL, Jing BY. On Blocking Rules For The Bootstrap With Dependent Data. Biometrika. 1995;82:561-74.
48. Stoye J, Evers D, Meyer F. Rose: generating sequence families. Bioinformatics. 1998;14:157-63.
49. Hasegawa M, Kishino H, Yano T-A. Dating Of The Human Ape Splitting By A Molecular Clock Of Mitochondrial-DNA. J Mol Evol. 1985;22:160-74.
50. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, et al. Ensembl 2013. Nucleic Acids Res. 2012;41:D48-55.