Phage cluster relationships identified through single gene analysis

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Smith, Kyle C ^a   Castro Nallar, Eduardo ^b   Fisher, Joshua N B ^a   Breakwell, Donald P ^a   Grose, Julianne H ^a   Burnett, Sandra H ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

^b GEORGE WASHINGTON UNIVERSITY   (United States)

Author keywords

Cluster; Coliphage; FFP; Mycobacteriophage; PCR; Phage genomics; Phylogeny; Subcluster

Indexed keywords

BACTERIAL DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; COLIPHAGE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE CLUSTER; GENE CONSTRUCT; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC SIMILARITY; MYCOBACTERIOPHAGE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SINGLE GENE ANALYSIS; SIPHOVIRUS COLIPHAGE; SPECIES COMPARISON; TMP GENE; UNINDEXED SEQUENCE;

BACTERIOPHAGES; BASE SEQUENCE; CLUSTER ANALYSIS; CONSERVED SEQUENCE; GENES, VIRAL; GENOMICS; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; VIRAL PROTEINS;

EID: 84879061415     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-410     Document Type: Article

References (40)

1. Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, et al. Expanding the diversity of Mycobacteriophages: Insights into genome architecture and evolution. PLoS One 2011, 6:1.
2. Hatfull GF. Mycobacteriophages: Genes and genomes. Annu Rev Microbiol 2010, 64(1):331-356. 10.1146/annurev.micro.112408.134233, 20528690.
3. Hendrix RW, Hatfull GF, Smith MCM. Bacteriophages with tails: chasing their origins and evolution. Res Microbiol 2003, 154(4):253-257. 10.1016/S0923-2508(03)00068-8, 12798229.
4. Hatfull GF. The secret lives of Mycobacteriophages. Adv Virus Res 2012, 82:179-288.
5. Casjens SR. Comparative genomics and evolution of the tailed-bacteriophages. Curr Opin Microbiol 2005, 8(4):451-458. 10.1016/j.mib.2005.06.014, 16019256.
6. Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philosophical Transactions of the Royal Society B: Biological Sciences 2008, 363(1512):4023-4029.
7. Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, et al. Comparative genomic analysis of 60 Mycobacteriophage Genomes: Genome clustering, gene acquisition, and gene size. J Mol Biol 2010, 397(1):119-143. 10.1016/j.jmb.2010.01.011, 2830324, 20064525.
8. Lawrence JG, Hatfull GF, Hendrix RW. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 2002, 184(17):4891-4905. 10.1128/JB.184.17.4891-4905.2002, 135278, 12169615.
9. Abuladze NK, Gingery M, Tsai J, Eiserling FA. Tail length determination in Bacteriophage-T4. Virology 1994, 199(2):301-310. 10.1006/viro.1994.1128, 8122363.
10. Belcaid M, Bergeron A, Poisson G. The evolution of the tape measure protein: units, duplications and losses. BMC Bioinforma 2011, 12(Suppl 9):S10.
11. Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM, Hryckowian AJ, Kelchner VA, et al. Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform. Plos Genet 2006, 2(6):835-847.
12. Krumsiek J, Arnold R, Rattei T. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007, 23(8):1026-1028. 10.1093/bioinformatics/btm039, 17309896.
13. Tetart F, Desplats C, Kutateladze M, Monod C, Ackermann HW, Krisch HM. Phylogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages. J Bacteriol 2001, 183(1):358-366. 10.1128/JB.183.1.358-366.2001, 94885, 11114936.
14. Comeau AM, Krisch HM. The Capsid of the T4 Phage Superfamily: The evolution, diversity, and structure of some of the most prevalent proteins in the biosphere. Mol Biol Evol 2008, 25(7):1321-1332. 10.1093/molbev/msn080, 18391067.
15. Cortines JR, Weigele PR, Gilcrease EB, Casjens SR, Teschke CM. Decoding bacteriophage P22 assembly: identification of two charged residues in scaffolding protein responsible for coat protein interaction. Virology 2011, 421(1):1-11. 10.1016/j.virol.2011.09.005, 3208733, 21974803.
16. Hauser R, Blasche S, Dokland T, Haggard-Ljungquist E, von Brunn A, Salas M, Casjens S, Molineux I, Uetz P. Bacteriophage protein-protein interactions. Adv Virus Res 2012, 83:219-298. 3461333, 22748812.
17. Rajagopala SV, Casjens S, Uetz P. The protein interaction map of bacteriophage lambda. BMC Microbiol 2011, 11:213. 10.1186/1471-2180-11-213, 3224144, 21943085.
18. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092, 17488738.
19. Jun SR, Sims GE, Wu GA, Kim SH. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Proc Natl Acad Sci U S A 2010, 107(1):133-138. 10.1073/pnas.0913033107, 2806744, 20018669.
20. Sims GE, Jun SR, Wu GA, Kim SH. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci U S A 2009, 106(8):2677-2682. 10.1073/pnas.0813249106, 2634796, 19188606.
21. Sims GE, Kim SH. Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc Natl Acad Sci U S A 2011, 108(20):8329-8334. 10.1073/pnas.1105168108, 3100984, 21536867.
22. Sousa A, Ze-Ze L, Silva P, Tenreiro R. Exploring tree-building methods and distinct molecular data to recover a known asymmetric phage phylogeny. Mol Phylogenet Evol 2008, 48(2):563-573. 10.1016/j.ympev.2008.04.030, 18524632.
23. Casjens SR, Thuman-Commike PA. Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology 2011, 411(2):393-415. 10.1016/j.virol.2010.12.046, 21310457.
24. Casjens SR. Diversity among the tailed-bacteriophages that infect the Enterobacteriaceae. Res Microbiol 2008, 159(5):340-348. 10.1016/j.resmic.2008.04.005, 2607141, 18550341.
25. Maddison WP. Gene trees in species trees. Syst Biol 1997, 46(3):523-536.
26. Pamilo P, Nei M. Relationships between gene trees and species trees. Mol Biol Evol 1988, 5(5):568-583.
27. Rosenberg NA. The probability of Topological concordance of gene trees and species trees. Theor Popul Biol 2002, 61(2):225-247. 10.1006/tpbi.2001.1568, 11969392.
28. Haggardljungquist E, Halling C, Calendar R. DNA-Sequences of the Tail Fiber Genes of Bacteriophage P2 - Evidence for Horizontal Transfer of Tail Fiber Genes among Unrelated Bacteriophages. J Bacteriol 1992, 174(5):1462-1477. 206541, 1531648.
29. Page RDM, Charleston MA. From gene to organismal phylogeny: Reconciled trees and the gene tree/Species tree problem. Molecular Phylogenetics and Evolution 1997, 7(2):231-240. 10.1006/mpev.1996.0390, 9126565.
30. Leaché AD, Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods. Syst Biol 2011, 60(2):126-137. 10.1093/sysbio/syq073, 21088009.
31. Rosenberg NA, Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet 2002, 3(5):380-390. 10.1038/nrg795, 11988763.
32. Hardies SC, Thomas JA, Serwer P. Comparative genomics of Bacillus thuringiensis phage 0305phi8-36: defining patterns of descent in a novel ancient phage lineage. Virol J 2007, 4:97. 10.1186/1743-422X-4-97, 2147016, 17919320.
33. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.
34. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012, 28(12):1647-1649. 10.1093/bioinformatics/bts199, 3371832, 22543367.
35. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Syst Biol 2012, 61(3):539-542. 10.1093/sysbio/sys029, 3329765, 22357727.
36. Posada D. jModelTest: Phylogenetic Model Averaging. Mol Biol Evol 2008, 25(7):1253-1256. 10.1093/molbev/msn083, 18397919.
37. Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) 2003, Sunderland, MA: Sinauer Associates.
38. Bogdanowicz D, Giaro K. Matching split distance for unrooted binary Phylogenetic trees. IEEE/ACM Trans Comput Biol Bioinform 2012, 9(1):150-160.
39. Bogdanowicz D, Giaro K, Wrobel B. TreeCmp: Comparison of trees in polynomial time. Evol Bioinform 2012, 8:475-487.
40. Cummings MP, Neel MC, Shaw KL. A genealogical approach to quantifying lineage divergence. Evolution 2008, 62(9):2411-2422. 10.1111/j.1558-5646.2008.00442.x, 18564377.