Genome sequencing of bacteria: Sequencing, de novo assembly and rapid analysis using open source tools

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Kisand, Veljo ^a,b   Lettieri, Teresa ^b  

^a UNIVERSITY OF TARTU   (Estonia)

^b JOINT RESEARCH CENTRE   (Italy)

Author keywords

Automated annotation; De novo assembly; De novo sequencing; Marine bacteria; Reference mapping

Indexed keywords

ALCANIVORAX; ALCANIVORAX BORKUMENSIS; ARTICLE; BACTERIAL GENOME; CODON; DNA FRAGMENTATION; GENE DELETION; GENE INSERTION; GENE MAPPING; GENE SEQUENCE; GENE TECHNOLOGY; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PYROSEQUENCING; SEQUENCE ANALYSIS;

ALCANIVORACEAE; ALGORITHMS; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA; SOFTWARE;

ALCANIVORAX BORKUMENSIS; BACTERIA (MICROORGANISMS); UNIDENTIFIED BACTERIUM;

EID: 84875483479     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-211     Document Type: Article

References (46)

1. DeLong E, Karl D. Genomic perspectives in microbial oceanography. Nature 2005, 437:336-342. 10.1038/nature04157, 16163343.
2. Loman N, Misra R, Dallman T, Constantinidou C, Gharbia S, Wain J, Pallen M. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012, 30:434-439. 10.1038/nbt.2198, 22522955.
3. Eddy S. Profile hidden Markov models. Bioinformatics 1998, 14:755-763. 10.1093/bioinformatics/14.9.755, 9918945.
4. Altschul S, Madden T, Schäffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
5. Poptsova M, Gogarten J. Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology 2010, 156:1909-1917. 10.1099/mic.0.033811-0, 20430813.
6. Siezen R, Van Hijum S. Genome (re-)annotation and open-source annotation pipelines. Microb Biotechnol 2010, 3:362-369. 10.1111/j.1751-7915.2010.00191.x, 21255336.
7. Integrated Microbial Genomes - Expert Review. http://img.jgi.doe.gov/er.
8. Prokaryotic Genomes Automatic Annotation Pipeline. http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html.
9. Rapid Annotation Transfer Tool. http://ratt.sourceforge.net/.
10. Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M, Meyer F, Olsen G, Olson R, Osterman A, Overbeek R, McNeil L, Paarmann D, Paczian T, Parrello B, Pusch G, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:Article number 75.
11. Overbeek R, Begley T, Butler R, Choudhuri J, Chuang H, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank E, Gerdes S, Glass E, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy A, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33:5691-5702. 10.1093/nar/gki866, 1251668, 16214803.
12. Markowitz V, Mavromatis K, Ivanova N, Chen I, Chu K, Kyrpides N. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009, 25:2271-2278. 10.1093/bioinformatics/btp393, 19561336.
13. Kisand V, Andersson N, Wikner J. Bacterial freshwater species successfully immigrate to the brackish water environment in the northern Baltic. Limnol Oceanogr 2005, 50:945-956.
14. Fraser C, Eisen J, Nelson K, Paulsen I, Salzberg S. The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol 2002, 184:6403-6405. 10.1128/JB.184.23.6403-6405.2002, 135419, 12426324.
15. Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly K, DeSalle R, Read T, Pop M. Finishing genomes with limited resources: Lessons from an ensemble of microbial genomes. BMC Genomics 2010, 11:242. 10.1186/1471-2164-11-242, 2864248, 20398345.
16. Bakke P, Carney N, DeLoache W, Gearing M, Ingvorsen K, Lotz M, McNair J, Penumetcha P, Simpson S, Voss L, Win M, Heyer L, Campbell A. Evaluation of three automated genome annotations for Halorhabdus utahensis. PLoS One 2009, 4(7):e6291. 10.1371/journal.pone.0006291, 2707008, 19617911.
17. Pevzner P, Tang H, Waterman M. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A 2001, 98:9748-9753. 10.1073/pnas.171285098, 55524, 11504945.
18. Zerbino D, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829. 10.1101/gr.074492.107, 2336801, 18349386.
19. Miller J, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010, 95:315-327. 10.1016/j.ygeno.2010.03.001, 2874646, 20211242.
20. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7:203-214. 10.1089/10665270050081478, 10890397.
21. The Marthlab: Mosaik. http://bioinformatics.bc.edu/marthlab/Mosaik.
22. Lowe T, Eddy S. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964. 146525, 9023104.
23. Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R, Smirnov S, Nikolskaya A, Rao B, Mekhedov S, Sverlov A, Vasudevan S, Wolf Y, Yin J, Natale D. The COG database: an updated vesion includes eukaryotes. BMC Bioinform 2003, 4:14. Article number 41.
24. Finn R, Tate J, Mistry J, Coggill P, Sammut S, Hotz H, Ceric G, Forslund K, Eddy S, Sonnhammer E, Bateman A. The Pfam protein families database. Nucleic Acids Res 2008, 36:D281-D288. 10.1093/nar/gkn226, 2238907, 18039703.
25. Klimke W, Agarwala R, Badretdin A, Chetvernin S, Ciufo S, Fedorov B, Kiryutin B, O'Neill K, Resch W, Resenchuk S, Schafer S, Tolstoy I, Tatusova T. The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res 2009, 37:D216-D223. 10.1093/nar/gkn734, 2686591, 18940865.
26. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:D480-D484. 2238879, 18077471.
27. Caspi R, Foerster H, Fulcher C, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee S, Shearer A, Tissier C, Walk T, Zhang P, Karp P. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2008, 36:D623-D631. 2238876, 17965431.
28. Salzberg S, Deicher A, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26:544-548. 10.1093/nar/26.2.544, 147303, 9421513.
29. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001, 29:2607-2618. 10.1093/nar/29.12.2607, 55746, 11410670.
30. Acinas S, Marcelino L, Klepac-Ceraj V, Polz M. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 2004, 186:2629-2635. 10.1128/JB.186.9.2629-2635.2004, 387781, 15090503.
31. Luo C, Hu G, Zhu H. Genome reannotation of Escherichia coli CFT073 with new insights into virulence. BMC Genomics 2009, 10:552. 10.1186/1471-2164-10-552, 2785843, 19930606.
32. Pinchuk G, Rodionov D, Yang C, Li X, Osterman A, Dervyn E, Geydebrekht O, Reed S, Romine M, Collart F, Scott J, Fredrickson J, Beliaev A. Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci U S A 2009, 106:2874-2879. 10.1073/pnas.0806798106, 2636740, 19196979.
33. Liolios K, Chen I, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz V, Kyrpides N. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010, 38:D346-D354. 10.1093/nar/gkp848, 2808860, 19914934.
34. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 2006, 103:12115-12120. 10.1073/pnas.0605127103, 1524930, 16880384.
35. Genomes Online Database. http://genomesonline.org/cgi-bin/GOLD/index.cgi.
36. Schneiker S, Dos Santos V, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova T, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina O, Kaminski F, Khachane A, Lang S, Linke B, McHardy A, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova J, Selbitschka W, Yakimov M, Timmis K, Vorhölter F, Weidner S, Kaiser O, Golyshin P. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 2006, 24:997-1004. 10.1038/nbt1232, 16878126.
37. Touchon M, Barbier P, Bernardet J, Loux V, Vacherie B, Barbe V, Rocha EPC, Duchaud E. Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl Environ Microbiol 2011, 77:7656-7662. 10.1128/AEM.05625-11, 3209149, 21926215.
38. McBride M, Xie G, Martens E, Lapidus A, Henrissat B, Rhodes R, Goltsman E, Wang W, Xu J, Hunnicutt D, Staroscik A, Hoover T, Cheng Y, Stein J. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009, 75:6864-6875. 10.1128/AEM.01495-09, 2772454, 19717629.
39. Duchaud E, Boussaha M, Loux V, Bernardet J, Michel C, Kerouault B, Mondot S, Nicolas P, Bossy R, Caron C, Bessieres P, Gibrat J, Claverol S, Dumetz F, Henaff M, Benmansour A. Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nat Biotechnol 2007, 25:763-769. 10.1038/nbt1313, 17592475.
40. Quinlan A, Stewart D, Strömberg M, Marth G. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 2008, 5:179-181. 10.1038/nmeth.1172, 18193056.
41. Pop M, Salzberg S. Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24:142-149. 10.1016/j.tig.2007.12.006, 2680276, 18262676.
42. Kisand V, Cuadros R, Wikner J. Phylogeny of Culturable Estuarine Bacteria Catabolizing Riverine Organic Matter in the N Baltic. Appl Environ Microbiol 2002, 68:379-388. 10.1128/AEM.68.1.379-388.2002, 126561, 11772648.
43. Kisand V, Wikner J. Combining culture-dependent and -independent methodologies for estimation of richness of estuarine bacterioplankton consuming riverine dissolved organic matter. Appl Environ Microbiol 2003, 69:3607-3616. 10.1128/AEM.69.6.3607-3616.2003, 161508, 12788769.
44. Mira Assembler. http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html.
45. Celera Assembler. http://wgs-assembler.sourceforge.net/.
46. Rapid Annotation Using Subsystem Technology. http://rast.nmpdr.org/.