Gegenees: Fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Ågren, Joakim ^a,b   Sundström, Anders ^a   Håfström, Therese ^a   Segerman, Bo ^a  

^a NATIONAL VETERINARY INSTITUTE   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACILLUS CEREUS; BACTERIAL GENOME; COMPUTER PROGRAM; CONTROLLED STUDY; ESCHERICHIA COLI; FOOT AND MOUTH DISEASE VIRUS; GENETIC CONSERVATION; INFORMATION PROCESSING; MICROBIAL GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENOMICS; SEQUENCE ALIGNMENT; VIRUS GENOME;

ALGORITHMS; BACILLUS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATA MINING; ESCHERICHIA COLI; FOOT-AND-MOUTH DISEASE VIRUS; GENE EXPRESSION PROFILING; GENOME; GENOMICS; PHYLOGENY; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84862503656     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039107     Document Type: Article

References (35)

1. Rokas A, Williams BL, King N, Carroll SB, (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
2. Jeffroy O, Brinkmann H, Delsuc F, Philippe H, (2006) Phylogenomics: the beginning of incongruence? Trends in genetics: TIG 22: 225-231.
3. Dubchak I, Poliakov A, Kislyuk A, Brudno M, (2009) Multiple whole-genome alignments without a reference organism. Genome research 19: 682-689.
4. Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, et al. (2011) Cactus: Algorithms for genome multiple sequence alignment. Genome research 21: 1512-1528.
5. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome research 14: 708-715.
6. Rausch T, Emde AK, Weese D, Doring A, Notredame C, et al. (2008) Segment-based multiple sequence alignment. Bioinformatics 24: i187-192.
7. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
8. Hohl M, Kurtz S, Ohlebusch E, (2002) Efficient multiple genome alignment. Bioinformatics 18: S312-320.
9. Angiuoli SV, Salzberg SL, (2011) Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27: 334-342.
10. Darling AE, Mau B, Perna NT, (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147.
11. Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, et al. (2007) Comprehensive DNA signature discovery and validation. PLoS Comput Biol 3: e98.
12. Rozen S, Skaletsky H, (2000) Primer3 on the WWW for general users and for biologist programmers. Methods in molecular biology 132: 365-386.
13. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
14. Segerman B, De Medici D, Ehling Schulz M, Fach P, Fenicia L, et al. (2011) Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain. Int J Food Microbiol 145: S167-176.
15. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC bioinformatics 10: 421.
16. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
17. Kolsto AB, Tourasse NJ, Okstad OA, (2009) What sets Bacillus anthracis apart from other Bacillus species? Annual review of microbiology 63: 451-476.
18. Tourasse NJ, Helgason E, Okstad OA, Hegna IK, Kolsto AB, (2006) The Bacillus cereus group: novel aspects of population structure and genome dynamics. Journal of applied microbiology 101: 579-593.
19. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution 28: 2731-2739.
20. Guinebretiere MH, Velge P, Couvert O, Carlin F, Debuyser ML, et al. (2010) Ability of Bacillus cereus group strains to cause food poisoning varies according to phylogenetic affiliation (groups I to VII) rather than species affiliation. Journal of clinical microbiology 48: 3388-3391.
21. Daffonchio D, Cherif A, Borin S, (2000) Homoduplex and heteroduplex polymorphisms of the amplified ribosomal 16 S-23 S internal transcribed spacers describe genetic relationships in the "Bacillus cereus group" Applied and environmental microbiology 66: 5460-5468.
22. Helgason E, Okstad OA, Caugant DA, Johansen HA, Fouet A, et al. (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis-one species on the basis of genetic evidence. Applied and environmental microbiology 66: 2627-2630.
23. Han CS, Xie G, Challacombe JF, Altherr MR, Bhotika SS, et al. (2006) Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. Journal of bacteriology 188: 3382-3390.
24. Klee SR, Brzuszkiewicz EB, Nattermann H, Bruggemann H, Dupke S, et al. (2010) The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS One 5: e10986.
25. Fricker M, Agren J, Segerman B, Knutsson R, Ehling-Schulz M, (2011) Evaluation of Bacillus strains as model systems for the work on Bacillus anthracis spores. International journal of food microbiology 145: S129-136.
26. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, et al. (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423: 81-86.
27. Sozhamannan S, Chute MD, McAfee FD, Fouts DE, Akmal A, et al. (2006) The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages. BMC microbiology 6: 34.
28. Wielinga PR, Hamidjaja RA, Agren J, Knutsson R, Segerman B, et al. (2011) A multiplex real-time PCR for identifying and differentiating B. anthracis virulent types. International journal of food microbiology 145: S137-144.
29. Gurumurthy CB, Sanyal A, Venkataramanan R, Tosh C, George M, et al. (2002) Genetic diversity in the VP1 gene of foot-and-mouth disease virus serotype Asia 1. Archives of virology 147: 85-102.
30. Carrillo C, Tulman ER, Delhon G, Lu Z, Carreno A, et al. (2005) Comparative genomics of foot-and-mouth disease virus. Journal of virology 79: 6487-6504.
31. Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, et al. (2011) Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104: H4 outbreak by rapid next generation sequencing technology. PLoS One 6: e22751.
32. Michino H, Araki K, Minami S, Takaya S, Sakai N, et al. (1999) Massive outbreak of Escherichia coli O157: H7 infection in schoolchildren in Sakai City, Japan, associated with consumption of white radish sprouts. American journal of epidemiology 150: 787-796.
33. Kulasekara BR, Jacobs M, Zhou Y, Wu Z, Sims E, et al. (2009) Analysis of the genome of the Escherichia coli O157: H7 2006 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence. Infection and immunity 77: 3713-3721.
34. Takahashi H, Shao M, Furuya N, Komano T, (2011) The genome sequence of the incompatibility group Igamma plasmid R621a: evolution of IncI plasmids. Plasmid 66: 112-121.
35. Tillier ER, Collins RA, (2000) Genome rearrangement by replication-directed translocation. Nat Genet 26: 195-197.