Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

Luhmann N, Dörr D, Chauve C (2017)
Microbial Genomics 3(9): e000123.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Luhmann, NinaUniBi ; Dörr, DanielUniBi ; Chauve, Cedric
Einrichtung
Technische Fakultät > Int. Graduiertenkolleg DiDy (GRK 1906)
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Graduate Center
Erscheinungsjahr
2017
Zeitschriftentitel
Microbial Genomics
Band
3
Ausgabe
9
Seite(n)
e000123
ISSN
2057-5858
Page URI
https://pub.uni-bielefeld.de/record/2912492

Zitieren

Luhmann N, Dörr D, Chauve C. Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics. 2017;3(9):e000123.
Luhmann, N., Dörr, D., & Chauve, C. (2017). Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics, 3(9), e000123. doi:10.1099/mgen.0.000123
Luhmann, Nina, Dörr, Daniel, and Chauve, Cedric. 2017. “Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes”. Microbial Genomics 3 (9): e000123.
Luhmann, N., Dörr, D., and Chauve, C. (2017). Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics 3, e000123.
Luhmann, N., Dörr, D., & Chauve, C., 2017. Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics, 3(9), p e000123.
N. Luhmann, D. Dörr, and C. Chauve, “Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes”, Microbial Genomics, vol. 3, 2017, pp. e000123.
Luhmann, N., Dörr, D., Chauve, C.: Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microbial Genomics. 3, e000123 (2017).
Luhmann, Nina, Dörr, Daniel, and Chauve, Cedric. “Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes”. Microbial Genomics 3.9 (2017): e000123.

57 References

Daten bereitgestellt von Europe PubMed Central.

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.
Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjogren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Ponten T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E., Cell 163(3), 2015
PMID: 26496604
Dynamics of genome rearrangement in bacterial populations.
Darling AE, Miklos I, Ragan MA., PLoS Genet. 4(7), 2008
PMID: 18650965
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis.
Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Medigue C, Simonet M, Chenal-Francisque V, Souza B, Dacheux D, Elliott JM, Derbise A, Hauser LJ, Garcia E., Proc. Natl. Acad. Sci. U.S.A. 101(38), 2004
PMID: 15358858
Ecological Opportunity, Evolution, and the Emergence of Flea-Borne Plague.
Hinnebusch BJ, Chouikha I, Sun YC., Infect. Immun. 84(7), 2016
PMID: 27160296
Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America.
Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, Bruce DC, Munk C, Brettin TS, Eppinger M, Ravel J, Wagner DM, Keim P., PLoS ONE 2(8), 2007
PMID: 17712418
Mind the gap; seven reasons to close fragmented genome assemblies.
Thomma BPHJ, Seidl MF, Shi-Kunne X, Cook DE, Bolton MD, van Kan JAL, Faino L., Fungal Genet. Biol. 90(), 2015
PMID: 26342853
The value of complete microbial genome sequencing (you get what you pay for).
Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL., J. Bacteriol. 184(23), 2002
PMID: 12426324
In defense of complete genomes.
Parkhill J., Nat. Biotechnol. 18(5), 2000
PMID: 10802612
Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation.
Klassen JL, Currie CR., BMC Genomics 13(), 2012
PMID: 22233127
Beware of mis-assembled genomes.
Salzberg SL, Yorke JA., Bioinformatics 21(24), 2005
PMID: 16332717
Genome assembly forensics: finding the elusive mis-assembly.
Phillippy AM, Schatz MC, Pop M., Genome Biol. 9(3), 2008
PMID: 18341692
Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.
Gasc C, Peyretaillade E, Peyret P., Nucleic Acids Res. 44(10), 2016
PMID: 27105841
Reconstructing ancient genomes and epigenomes.
Orlando L, Gilbert MT, Willerslev E., Nat. Rev. Genet. 16(7), 2015
PMID: 26055157
Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects.
Yoshida K, Sasaki E, Kamoun S., Front Plant Sci 6(), 2015
PMID: 26442080
Introduction. Ancient DNA: the first three decades.
Hagelberg E, Hofreiter M, Keyser C., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 370(1660), 2015
PMID: 25487324
The future of ancient DNA: Technical advances and conceptual shifts.
Hofreiter M, Paijmans JL, Goodchild H, Speller CF, Barlow A, Fortes GG, Thomas JA, Ludwig A, Collins MJ., Bioessays 37(3), 2014
PMID: 25413709
Genetic analyses from ancient DNA.
Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M., Annu. Rev. Genet. 38(), 2004
PMID: 15568989
Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.
Martin MD, Cappellini E, Samaniego JA, Zepeda ML, Campos PF, Seguin-Orlando A, Wales N, Orlando L, Ho SY, Dietrich FS, Mieczkowski PA, Heitman J, Willerslev E, Krogh A, Ristaino JB, Gilbert MT., Nat Commun 4(), 2013
PMID: 23863894
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine.
Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, Thines M, Weigel D, Burbano HA., Elife 2(), 2013
PMID: 23741619
Recovery of a medieval Brucella melitensis genome using shotgun metagenomics.
Kay GL, Sergeant MJ, Giuffra V, Bandiera P, Milanese M, Bramanti B, Bianucci R, Pallen MJ., MBio 5(4), 2014
PMID: 25028426
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.
Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Bastida R, Huson D, Nieselt K, Young D, Parkhill J, Buikstra JE, Gagneux S, Stone AC, Krause J., Nature 514(7523), 2014
PMID: 25141181
Genome-wide comparison of medieval and modern Mycobacterium leprae.
Schuenemann VJ, Singh P, Mendum TA, Krause-Kyora B, Jager G, Bos KI, Herbig A, Economou C, Benjak A, Busso P, Nebel A, Boldsen JL, Kjellstrom A, Wu H, Stewart GR, Taylor GM, Bauer P, Lee OY, Wu HH, Minnikin DE, Besra GS, Tucker K, Roffey S, Sow SO, Cole ST, Nieselt K, Krause J., Science 341(6142), 2013
PMID: 23765279
The 5300-year-old Helicobacter pylori genome of the Iceman.
Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, Kusebauch U, Vigl EE, Malfertheiner P, Megraud F, O'Sullivan N, Cipollini G, Coia V, Samadelli M, Engstrand L, Linz B, Moritz RL, Grimm R, Krause J, Nebel A, Moodley Y, Rattei T, Zink A., Science 351(6269), 2016
PMID: 26744403
Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849.
Devault AM, Golding GB, Waglechner N, Enk JM, Kuch M, Tien JH, Shi M, Fisman DN, Dhody AN, Forrest S, Bos KI, Earn DJ, Holmes EC, Poinar HN., N. Engl. J. Med. 370(4), 2014
PMID: 24401020
Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis.
Wagner DM, Klunk J, Harbeck M, Devault A, Waglechner N, Sahl JW, Enk J, Birdsell DN, Kuch M, Lumibao C, Poinar D, Pearson T, Fourment M, Golding B, Riehm JM, Earn DJ, Dewitte S, Rouillard JM, Grupe G, Wiechmann I, Bliska JB, Keim PS, Scholz HC, Holmes EC, Poinar H., Lancet Infect Dis 14(4), 2014
PMID: 24480148
A draft genome of Yersinia pestis from victims of the Black Death.
Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, DeWitte SN, Meyer M, Schmedes S, Wood J, Earn DJ, Herring DA, Bauer P, Poinar HN, Krause J., Nature 478(7370), 2011
PMID: 21993626
Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus.
Bos KI, Herbig A, Sahl J, Waglechner N, Fourment M, Forrest SA, Klunk J, Schuenemann VJ, Poinar D, Kuch M, Golding GB, Dutour O, Keim P, Wagner DM, Holmes EC, Krause J, Poinar HN., Elife 5(), 2016
PMID: 26795402
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
Schubert M, Ermini L, Der Sarkissian C, Jonsson H, Ginolhac A, Schaefer R, Martin MD, Fernandez R, Kircher M, McCue M, Willerslev E, Orlando L., Nat Protoc 9(5), 2014
PMID: 24722405
EAGER: efficient ancient genome reconstruction.
Peltzer A, Jager G, Herbig A, Seitz A, Kniep C, Krause J, Nieselt K., Genome Biol. 17(), 2016
PMID: 27036623
Reordering contigs of draft genomes using the Mauve aligner.
Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT., Bioinformatics 25(16), 2009
PMID: 19515959
FPSAC: fast phylogenetic scaffolding of ancient contigs.
Rajaraman A, Tannier E, Chauve C., Bioinformatics 29(23), 2013
PMID: 24068034
Ragout-a reference-assisted assembly tool for bacterial genomes.
Kolmogorov M, Raney B, Paten B, Pham S., Bioinformatics 30(12), 2014
PMID: 24931998
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lio P, Crescenzi P, Fani R, Fondi M., Bioinformatics 31(15), 2015
PMID: 25810435
'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution.
McNally A, Thomson NR, Reuter S, Wren BW., Nat. Rev. Microbiol. 14(3), 2016
PMID: 26876035
Toward defining the course of evolution: minimum change for a specific tree topology
Fitch WM., 1971
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168
A note on two problems in connexion with graphs
Dijkstra EW., 1959
Bacterial genome instability.
Darmon E, Leach DR., Microbiol. Mol. Biol. Rev. 78(1), 2014
PMID: 24600039
Space-efficient and exact de Bruijn graph representation based on a Bloom filter.
Chikhi R, Rizk G., Algorithms Mol Biol 8(1), 2013
PMID: 24040893
BASys: a web server for automated bacterial genome annotation.
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980511
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC., Nucleic Acids Res. 32(5), 2004
PMID: 15034147
A new generation of homology search tools based on probabilistic inference.
Eddy SR., Genome Inform 23(1), 2009
PMID: 20180275
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM., PLoS ONE 9(11), 2014
PMID: 25409509
Genetic analyses from ancient DNA.
Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M., Annu. Rev. Genet. 38(), 2004
PMID: 15568989
A unifying view of genome rearrangements
Bergeron A, Mixtacki J, Stoye J., 2006
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E., Genome Res. 18(5), 2008
PMID: 18349386
Versatile and open software for comparing large genomes.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL., Genome Biol. 5(2), 2004
PMID: 14759262
Automated ensemble assembly and validation of microbial genomes.
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM., BMC Bioinformatics 15(), 2014
PMID: 24884846
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA., J. Comput. Biol. 19(5), 2012
PMID: 22506599
Gap Filling as Exact Path Length Problem.
Salmela L, Sahlin K, Makinen V, Tomescu AI., J. Comput. Biol. 23(5), 2016
PMID: 26959081
De novo likelihood-based measures for comparing genome assemblies.
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M., BMC Res Notes 6(), 2013
PMID: 23965294
CGAL: computing genome assembly likelihoods.
Rahman A, Pachter L., Genome Biol. 14(1), 2013
PMID: 23360652
Quantitative assessment of insertion sequence impact on bacterial genome architecture.
Adams MD, Bishop B, Wright MS., Microb Genom 2(7), 2016
PMID: 28348858
ISfinder: the reference centre for bacterial insertion sequences.
Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381877
gargammel: a sequence simulator for ancient DNA.
Renaud G, Hanghoj K, Willerslev E, Orlando L., Bioinformatics 33(4), 2017
PMID: 27794556
Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics.
Spyrou MA, Tukhbatova RI, Feldman M, Drath J, Kacki S, Beltran de Heredia J, Arnold S, Sitdikov AG, Castex D, Wahl J, Gazimzyanov IR, Nurgaliev DK, Herbig A, Bos KI, Krause J., Cell Host Microbe 19(6), 2016
PMID: 27281573
Circos: an information aesthetic for comparative genomics.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA., Genome Res. 19(9), 2009
PMID: 19541911
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