Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq

Frontiers in Genetics

Volumn 5, Issue JAN, 2015, Pages

  Deatherage, Daniel E ^a   Traverse, Charles C ^a   Wolf, Lindsey N ^a   Barrick, Jeffrey E ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Evolutionary dead end; Experimental evolution; Genetic parallelism; Genome resequencing; Insertion sequence

Indexed keywords

ARTICLE; FABR GENE; GAIN OF FUNCTION MUTATION; GENE FREQUENCY; GENE INSERTION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC POLYMORPHISM; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; HUMAN; INDEL MUTATION; LONG TERM EVOLUTION EXPERIMENT; MATHEMATICAL MODEL; MRAZ GENE; MUTATIONAL ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURAL VARIATION;

ESCHERICHIA COLI;

EID: 84923250136     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00468     Document Type: Article

References (54)

1. Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., et al. (2011). Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12:R18. doi: 10.1186/gb-2011-12-2-r18
2. Barrick, J. E., Colburn, G., Deatherage, D. E., Traverse, C. C., Strand, M. D., Borges, J. J., et al. (2014). Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15:1039. doi: 10.1186/1471-2164-15-1039
3. Barrick, J. E., and Lenski, R. E. (2009). Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb. Symp. Quant. Biol. 74, 119-129. doi: 10.1101/sqb.2009.74.018
4. Barrick, J. E., and Lenski, R. E. (2013). Genome dynamics during experimental evolution. Nat. Rev. Genet. 14, 827-839. doi: 10.1038/nrg3564
5. Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., et al. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243-1247. doi: 10.1038/nature08480
6. Barroso-Batista, J., Sousa, A., Lourenço, M., Bergman, M. -L., Sobral, D., Demengeot, J., et al. (2014). The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet. 10:e1004182. doi: 10.1371/journal.pgen.1004182
7. Blount, Z. D., Barrick, J. E., Davidson, C. J., and Lenski, R. E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489, 513-518. doi: 10.1038/nature11514
8. Blount, Z. D., Borland, C. Z., and Lenski, R. E. (2008). Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 105, 7899-7906. doi: 10.1073/pnas.0803151105
9. Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120. doi: 10.1093/bioinformatics/btu170
10. Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., et al. (2009). BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677-681. doi: 10.1038/nmeth.1363
11. Chubiz, L. M., Lee, M.-C., Delaney, N. F., and Marx, C. J. (2012). FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations. PLoS ONE 7:e47959. doi: 10.1371/journal.pone.0047959
12. Conrad, T. M., Lewis, N. E., and Palsson, B. O. (2011). Microbial laboratory evolution in the era of genome-scale science. Mol. Syst. Biol. 7, 509. doi: 10.1038/msb.2011.42
13. Cooper, V. S., Schneider, D., Blot, M., and Lenski, R. E. (2001). Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J. Bacteriol. 183, 2834-2841. doi: 10.1128/JB.183.9.2834-2841.2001
14. Daubin, V., Lerat, E., and Perrière, G. (2003). The source of laterally transferred genes in bacterial genomes. Genome Biol. 4:R57. doi: 10.1186/gb-2003-4-9-r57
15. Deatherage, D. E., and Barrick, J. E. (2014). Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165-188. doi: 10.1007/978-1-4939-0554-6_12
16. Deininger, M., Goldman, J., and Melo, J. (2000). The molecular biology of chronic myeloid leukemia. Blood 96, 3343-3356.
17. Dodt, M., Roehr, J., Ahmed, R., and Dieterich, C. (2012). FLEXBAR-Flexible barcode and adapter processing for next-generation sequencing platforms. Biology (Basel) 1, 895-905. doi: 10.3390/biology1030895
18. Dunham, M. J., Badrane, H., Ferea, T., Adams, J., Brown, P. O., Rosenzweig, F., et al. (2002). Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 99, 16144-16149. doi: 10.1073/pnas.242624799
19. Eraso, J. M., Markillie, L. M., Mitchell, H. D., Taylor, R. C., Orr, G., and Margolin, W. (2014). The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli. J. Bacteriol. 196, 2053-2066. doi: 10.1128/JB.01370-13
20. Ge, H., Liu, K., Juan, T., Fang, F., Newman, M., and Hoeck, W. (2011). FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics 27, 1922-1928. doi: 10.1093/bioinformatics/btr310
21. Gresham, D., Desai, M. M., Tucker, C. M., Jenq, H. T., Pai, D. A., Ward, A., et al. (2008). The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4:e1000303. doi: 10.1371/journal.pgen.1000303
22. Herron, M. D., and Doebeli, M. (2013). Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLoS Biol. 11:e1001490. doi: 10.1371/journal.pbio.1001490
23. Holtgrewe, M. (2010). Mason - A Read Simulator for Second Generation Sequencing Data. Institut für Mathematik und Informatik, Freie Universität Berlin, Berlin.
24. Hormozdiari, F., Hajirasouliha, I., Dao, P., Hach, F., Yorukoglu, D., Alkan, C., et al. (2010). Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26, i350-i357. doi: 10.1093/bioinformatics/btq216
25. Jeong, H., Barbe, V., Lee, C. H., Vallenet, D., Yu, D. S., Choi, S.-H., et al. (2009). Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J. Mol. Biol. 394, 644-652. doi: 10.1016/j.jmb.2009.09.052
26. Khan, A. I., Dinh, D. M., Schneider, D., Lenski, R. E., and Cooper, T. F. (2011). Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332, 1193-1196. doi: 10.1126/science.1203801
27. Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and Salzberg, S. L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14:R36. doi: 10.1186/gb-2013-14-4-r36
28. Kim, D., and Salzberg, S. L. (2011). TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol. 12:R72. doi: 10.1186/gb-2011-12-8-r72
29. Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., et al. (2004). Versatile and open software for comparing large genomes. Genome Biol. 5:R12. doi: 10.1186/gb-2004-5-2-r12
30. Lang, G. I., Rice, D. P., Hickman, M. J., Sodergren, E., Weinstock, G. M., Botstein, D., et al. (2013). Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500, 571-574. doi: 10.1038/nature12344
31. Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-360. doi: 10.1038/nmeth.1923
32. Lenski, R. E., Rose, M. R., Simpson, S. C., and Tadler, S. C. (1991). Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am. Nat. 138, 1315-1341. doi: 10.1086/285289
33. Lenski, R. E., and Travisano, M. (1994). Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Natl. Acad. Sci. U.S.A. 91, 6808-6814. doi: 10.1073/pnas.91.15.6808
34. Lou, D. I., Hussmann, J. A., McBee, R. M., Acevedo, A., Andino, R., Press, W. H., et al. (2013). High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc. Natl. Acad. Sci. U.S.A. 110, 19872-19877. doi: 10.1073/pnas.1319590110
35. Philippe, N., Crozat, E., Lenski, R. E., and Schneider, D. (2007). Evolution of global regulatory networks during a long-term experiment with Escherichia coli. Bioessays 29, 846-860. doi: 10.1002/bies.20629
36. Philippe, N., Pelosi, L., Lenski, R. E., and Schneider, D. (2009). Evolution of penicillin-binding protein 2 concentration and cell shape during a long-term experiment with Escherichia coli. J. Bacteriol. 191, 909-921. doi: 10.1128/JB.01419-08
37. Quandt, E. M., Deatherage, D. E., Ellington, A. D., Georgiou, G., and Barrick, J. E. (2013). Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 111, 2217-2222
38. Raeside, C., Gaffé, J., Deatherage, D. E., Tenaillon, O., Briska, A. M., Ptashkin, R. N., et al. (2014). Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. MBio 5, e01377-e01314. doi: 10.1128/mBio.01377-14
39. R Core Team. (2014). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna. Available online at: at: http://www.r-project.org/.
40. Rozen, D. E., Schneider, D., and Lenski, R. E. (2005). Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J. Mol. Evol. 61, 171-180. doi: 10.1007/s00239-004-0322-2
41. Sboner, A., Habegger, L., Pflueger, D., Terry, S., Chen, D. Z., Rozowsky, J. S., et al. (2010). FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol. 11:R104. doi: 10.1186/gb-2010-11-10-r104
42. Schloss, P. D., Gevers, D., and Westcott, S. L. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6:e27310. doi: 10.1371/journal.pone.0027310
43. Schmitt, M. W., Kennedy, S. R., Salk, J. J., Fox, E. J., Hiatt, J. B., and Loeb, L. A. (2012). Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl. Acad. Sci. U.S.A. 109, 14508-14513. doi: 10.1073/pnas.1208715109
44. Stanek, M. T., Cooper, T. F., and Lenski, R. E. (2009). Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli. BMC Evol. Biol. 9:302. doi: 10.1186/1471-2148-9-302
45. Tenaillon, O., Rodríguez-Verdugo, A., Gaut, R. L., McDonald, P., Bennett, A. F., Long, A. D., et al. (2012). The molecular diversity of adaptive convergence. Science 335, 457-461. doi: 10.1126/science.1212986
46. Traverse, C. C., Mayo-Smith, L. M., Poltak, S. R., and Cooper, V. S. (2013). Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. Proc. Natl. Acad. Sci. U.S.A. 110, E250-E259. doi: 10.1073/pnas.1207025110
47. Wielgoss, S., Barrick, J. E., Tenaillon, O., Cruveiller, S., Chane-Woon-Ming, B., Medigue, C., et al. (2011). Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. G3 Genes Genomes Genet. 1, 183-186. doi: 10.1534/g3.111.000406
48. Wielgoss, S., Barrick, J. E., Tenaillon, O., Wiser, M. J., Dittmar, W. J., Cruveiller, S., et al. (2013). Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proc. Natl. Acad. Sci. U.S.A. 110, 222-227. doi: 10.1073/pnas.1219574110
49. Woodman, C. B. J., Collins, S. I., and Young, L. S. (2007). The natural history of cervical HPV infection: unresolved issues. Nat. Rev. Cancer 7, 11-22. doi: 10.1038/nrc2050
50. Woods, R. J., Barrick, J. E., Cooper, T. F., Shrestha, U., Kauth, M. R., and Lenski, R. E. (2011). Second-order selection for evolvability in a large Escherichia coli population. Science 331, 1433-1436. doi: 10.1126/science.1198914
51. Woods, R., Schneider, D., Winkworth, C. L., Riley, M. A., and Lenski, R. E. (2006). Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103, 9107-9112. doi: 10.1073/pnas.0602917103
52. Yang, L., Luquette, L. J., Gehlenborg, N., Xi, R., Haseley, P. S., Hsieh, C.-H., et al. (2013). Diverse mechanisms of somatic structural variations in human cancer genomes. Cell 153, 919-929. doi: 10.1016/j.cell.2013.04.010
53. Zeitouni, B., Boeva, V., Janoueix-Lerosey, I., Loeillet, S., Legoix-né, P., Nicolas, A., et al. (2010). SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics 26, 1895-1896. doi: 10.1093/bioinformatics/btq293
54. Zhu, K., Zhang, Y.-M., and Rock, C. O. (2009). Transcriptional regulation of membrane lipid homeostasis in Escherichia coli. J. Biol. Chem. 284, 34880-34888. doi: 10.1074/jbc. M109.068239