Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation

Kahlke T, Goesmann A, Hjerde E, Willassen NP, Haugen P (2012)
BMC genomics 13(1): 179.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ;
Abstract / Bemerkung
ABSTRACT: BACKGROUND: The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups. RESULTS: The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin. CONCLUSION: The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.
Erscheinungsjahr
Zeitschriftentitel
BMC genomics
Band
13
Ausgabe
1
Seite(n)
179
ISSN
PUB-ID

Zitieren

Kahlke T, Goesmann A, Hjerde E, Willassen NP, Haugen P. Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation. BMC genomics. 2012;13(1):179.
Kahlke, T., Goesmann, A., Hjerde, E., Willassen, N. P., & Haugen, P. (2012). Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation. BMC genomics, 13(1), 179. doi:10.1186/1471-2164-13-179
Kahlke, T., Goesmann, A., Hjerde, E., Willassen, N. P., and Haugen, P. (2012). Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation. BMC genomics 13, 179.
Kahlke, T., et al., 2012. Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation. BMC genomics, 13(1), p 179.
T. Kahlke, et al., “Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation”, BMC genomics, vol. 13, 2012, pp. 179.
Kahlke, T., Goesmann, A., Hjerde, E., Willassen, N.P., Haugen, P.: Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation. BMC genomics. 13, 179 (2012).
Kahlke, Tim, Goesmann, Alexander, Hjerde, Erik, Willassen, Nils Peder, and Haugen, Peik. “Unique core genomes of the bacterial family vibrionaceae: Insights into niche adaptation and speciation”. BMC genomics 13.1 (2012): 179.

11 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A genomic view of food-related and probiotic Enterococcus strains.
Bonacina J, Suárez N, Hormigo R, Fadda S, Lechner M, Saavedra L., DNA Res 24(1), 2017
PMID: 27773878
Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing.
Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF., Genome Biol Evol 9(12), 2017
PMID: 29194487
Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat.
Liu M, Stiller J, Holušová K, Vrána J, Liu D, Doležel J, Liu C., Sci Rep 6(), 2016
PMID: 27821854
Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria.
Lòpez-Fernàndez S, Sonego P, Moretto M, Pancher M, Engelen K, Pertot I, Campisano A., Front Microbiol 6(), 2015
PMID: 26074885
Insights into the maize pan-genome and pan-transcriptome.
Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Peñagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR., Plant Cell 26(1), 2014
PMID: 24488960
Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae.
Siewert C, Hess WR, Duduk B, Huettel B, Reinhardt R, Büttner C, Kube M., BMC Genomics 15(), 2014
PMID: 25344468
Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica.
Gordienko EN, Kazanov MD, Gelfand MS., J Bacteriol 195(12), 2013
PMID: 23585535

46 References

Daten bereitgestellt von Europe PubMed Central.

Defining pathogenic bacterial species in the genomic era
AUTHOR UNKNOWN, 2011
Genomics of epidemic pathogens
AUTHOR UNKNOWN, 2011
What are bacterial species?
Cohan FM., Annu. Rev. Microbiol. 56(), 2002
PMID: 12142474
Measuring genome evolution.
Huynen MA, Bork P., Proc. Natl. Acad. Sci. U.S.A. 95(11), 1998
PMID: 9600883
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM., Proc. Natl. Acad. Sci. U.S.A. 102(39), 2005
PMID: 16172379
Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome.
Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D, Tatusova T, Parkhill J, Bentley SD, Post JC, Ehrlich GD, Hu FZ., J. Bacteriol. 189(22), 2007
PMID: 17675389
The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J., J. Bacteriol. 190(20), 2008
PMID: 18676672
On the origins of a Vibrio species.
Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW., Microb. Ecol. 59(1), 2010
PMID: 19830476
Estimating the size of the bacterial pan-genome.
Lapierre P, Gogarten JP., Trends Genet. 25(3), 2009
PMID: 19168257
The microbial pan-genome.
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R., Curr. Opin. Genet. Dev. 15(6), 2005
PMID: 16185861
The bacterial species dilemma and the genomic-phylogenetic species concept.
Staley JT., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 361(1475), 2006
PMID: 17062409
What makes pathogens pathogenic
AUTHOR UNKNOWN, 2008
Signature genes as a phylogenomic tool.
Dutilh BE, Snel B, Ettema TJ, Huynen MA., Mol. Biol. Evol. 25(8), 2008
PMID: 18492663

AUTHOR UNKNOWN, 2011
Identifying bacterial genes and endosymbiont DNA with Glimmer.
Delcher AL, Bratke KA, Powers EC, Salzberg SL., Bioinformatics 23(6), 2007
PMID: 17237039
The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.
Hjerde E, Lorentzen MS, Holden MT, Seeger K, Paulsen S, Bason N, Churcher C, Harris D, Norbertczak H, Quail MA, Sanders S, Thurston S, Parkhill J, Willassen NP, Thomson NR., BMC Genomics 9(), 2008
PMID: 19099551
OrthoMCL: identification of ortholog groups for eukaryotic genomes.
Li L, Stoeckert CJ Jr, Roos DS., Genome Res. 13(9), 2003
PMID: 12952885
Gene sequences useful for predicting relatedness of whole genomes in bacteria.
Zeigler DR., Int. J. Syst. Evol. Microbiol. 53(Pt 6), 2003
PMID: 14657120
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088
EPoS: a modular software framework for phylogenetic analysis.
Griebel T, Brinkmeyer M, Bocker S., Bioinformatics 24(20), 2008
PMID: 18632748
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck JP, Ronquist F., Bioinformatics 17(8), 2001
PMID: 11524383
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Ronquist F, Huelsenbeck JP., Bioinformatics 19(12), 2003
PMID: 12912839
Comparison of phylogenetic trees
AUTHOR UNKNOWN, 1981
Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity.
Le Roux F, Zouine M, Chakroun N, Binesse J, Saulnier D, Bouchier C, Zidane N, Ma L, Rusniok C, Lajus A, Buchrieser C, Medigue C, Polz MF, Mazel D., Environ. Microbiol. 11(8), 2009
PMID: 19364337
O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates.
Wildschutte H, Preheim SP, Hernandez Y, Polz MF., Environ. Microbiol. 12(11), 2010
PMID: 20629700
The tcp gene cluster of Vibrio cholerae.
Manning PA., Gene 192(1), 1997
PMID: 9224875
Diversity in chemotaxis mechanisms among the bacteria and archaea.
Szurmant H, Ordal GW., Microbiol. Mol. Biol. Rev. 68(2), 2004
PMID: 15187186
Characterization of Vibrio cholerae aerotaxis.
Boin MA, Hase CC., FEMS Microbiol. Lett. 276(2), 2007
PMID: 17956426
Bacterial energy taxis: a global strategy?
AUTHOR UNKNOWN, 2010
Vibriobactin, a siderophore from Vibrio cholerae.
Griffiths GL, Sigel SP, Payne SM, Neilands JB., J. Biol. Chem. 259(1), 1984
PMID: 6706943
Iron acquisition in Vibrio cholerae.
Wyckoff EE, Mey AR, Payne SM., Biometals 20(3-4), 2007
PMID: 17216354
VibD and VibH are required for late steps in vibriobactin biosynthesis in Vibrio cholerae.
Wyckoff EE, Smith SL, Payne SM., J. Bacteriol. 183(5), 2001
PMID: 11160122
Massive comparative genomic analysis reveals convergent evolution of specialized bacteria.
Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D., Biol. Direct 4(), 2009
PMID: 19361336
Opinion: Re-evaluating prokaryotic species.
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J., Nat. Rev. Microbiol. 3(9), 2005
PMID: 16138101
Sequencing the species pan-genome
AUTHOR UNKNOWN, 2009
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes
AUTHOR UNKNOWN, 2007
From Gene Trees to Organismal Phylogeny in Prokaryotes: The Case of the g-Proteobacteria
AUTHOR UNKNOWN, 2003
Genomic taxonomy of Vibrios.
Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N Jr, Ussery DW, Iida T, Thompson FL., BMC Evol. Biol. 9(), 2009
PMID: 19860885
Phylogenetics and the cohesion of bacterial genomes.
Daubin V, Moran NA, Ochman H., Science 301(5634), 2003
PMID: 12907801

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 22574681
PubMed | Europe PMC

Suchen in

Google Scholar