Re-annotation of protein-coding genes in 10 complete genomes of neisseriaceae family by combining similarity-based and composition-based methods

DNA Research

Volumn 20, Issue 3, 2013, Pages 273-286

  Guo, Feng Biao ^a,b   Xiong, Lifeng ^a   Teng, Jade L L ^a   Yuen, Kwok Yung ^a,c   Lau, Susanna K P ^a,c   Woo, Patrick C Y ^a,c  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c THE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Eliminated non coding ORFs; Newly assigned functions; Newly found genes; Re annotation; The Neisseriaceae family

Indexed keywords

ALGORITHM; ARCHAEAL GENOME; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL SURVIVAL; CHROMOBACTERIUM VIOLACEUM; CODON; DNA SEQUENCE; DNA STRAND; GENETIC ANALYSIS; NEISSERIACEAE; NONHUMAN; PREDICTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ELIMINATED NON-CODING ORFS; NEWLY ASSIGNED FUNCTIONS; NEWLY FOUND GENES; RE-ANNOTATION; THE NEISSERIACEAE FAMILY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE COMPOSITION; DNA, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; NEISSERIACEAE; OPEN READING FRAMES; TRANSCRIPTION, GENETIC; TRANSPOSASES;

EID: 84884186033     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst009     Document Type: Article

References (44)

1. Ouzounis, C.A. and Karp, P.D. 2002, The past, present and future of genome-wide re-annotation, Genome Biol., 3, COMMENT2001.
2. van den Berg, B.H., McCarthy, F.M., Lamont, S.J. and Burgess, S.C. 2010, Re-annotation is an essential step in systems biology modeling of functional genomics data, PLoS One, 5, e10642.
3. Wang, J. and Zhang, C.T. 2001, Identification of proteincoding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotides, Eur. J. Biochem., 268, 4261-8.
4. Kawarabayasi, Y., Hino, Y., Horikawa, H., et al. 1999, Complete genome sequence of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1, DNA Res., 6, 83-101, 145-52.
5. Natale, D.A., Shankavaram, U.T., Galperin, M.Y., Wolf, Y.I., Aravind, L. and Koonin, E.V. 2000, Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs), Genome Biol., 1, RESEARCH0009.
6. Bocs, S., Danchin, A. and Medigue, C. 2002, Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes, BMC Bioinformatics, 3, 5.
7. Guo, F.B., Wang, J. and Zhang, C.T. 2004, Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1, DNA Res., 11, 361-70.
8. Yamazaki, S., Yamazaki, J., Nishijima, K., et al. 2006, Proteome analysis of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1, Mol. Cell. Proteomics, 5, 811-23.
9. Guo, F.B. and Lin, Y. 2009, Identify protein-coding genes in the genomes of Aeropyrum pernix K1 and Chlorobium tepidum TLS, J. Biomol. Struct. Dyn., 26, 413-20.
10. Yu, J.F., Jiang, D.K., Xiao, K., Jin, Y., Wang, J.H. and Sun, X. 2012, Discriminate the falsely predicted proteincoding genes in Aeropyrum Pernix K1 genome based on graphical representation, MATCH Commun. Math. Comput. Chem., 67, 845-66.
11. Bawden, A.L., Glassberg, K.J., Diggans, J., Shaw, R., Farmerie, W. and Moyer, R.W. 2000, Complete genomic sequence of the Amsacta moorei entomopoxvirus: analysis and comparison with other poxviruses, Virology, 274, 120-39.
12. Guo, F.B. and Yu, X.J. 2007, Re-prediction of proteincoding genes in the genome of Amsacta moorei entomopoxvirus, J. Virol. Methods, 146, 389-92.
13. Yu, J.F. and Sun, X. 2010, Reannotation of proteincoding genes based on an improved graphical representation of DNA sequence, J. Comput. Chem., 31, 2126-35.
14. Zhou, L., Vorhölter, F.J., He, Y.Q., et al. 2011, Gene discovery by genome-wide CDS re-prediction and microarray- based transcriptional analysis in phytopathogen Xanthomonas campestris, BMC Genomics, 12, 359.
15. Du, M.Z., Guo, F.B. and Chen, Y.Y. 2011, Gene re-annotation in genome of the extremophile Pyrobaculum aerophilum by using bioinformatics methods, J. Biomol. Struct. Dyn., 29, 391-401.
16. Chen, L.L., Ma, B.G. and Gao, N. 2008, Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043, FEBS J., 275, 198-206.
17. Okamoto, A. and Yamada, K. 2011, Proteome driven reevaluation and functional annotation of the Streptococcus pyogenes SF370 genome, BMC Microbiol., 11, 249.
18. Tettelin, H., Saunders, N.J., Heidelberg, J., et al. 2000, Complete genome sequence of Neisseria meningitidis serogroup B strain MC58, Science, 287, 1809-15.
19. Yuen, K.Y., Woo, P.C., Teng, J.L., Leung, K.W., Wong, M.K. and Lau, S.K. 2001, Laribacter hongkongensis gen. nov., sp. nov., a novel Gram-negative bacterium isolated from a cirrhotic patient with bacteremia and empyema, J. Clin. Microbiol., 39, 4227-32.
20. Woo, P.C., Lau, S.K., Teng, J.L., et al. 2004, Association of Laribacter hongkongensis in community-acquired gastroenteritis with travel and eating fish: a multicentre case-control study, Lancet, 363, 1941-7.
21. Woo, P.C., Lau, S.K., Tse, H., et al. 2009, The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats, PLoS Genet., 25, e1000416.
22. Kim, D.S., Wi, Y.M., Choi, J.Y., Peck, K.R., Song, J.H. and Ko, K.S. 2011, Bacteremia caused by Laribacter hongkongensis misidentified as Acinetobacter lwoffii: report of the first case in Korea, J. Korean Med. Sci., 26, 679-81.
23. Pagani, I., Liolios, K., Jansson, J., et al. 2012, The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata, Nucleic Acids Res., 40, D571-9.
24. Pruitt, K.D., Tatusova, T. and Maglott, D.R. 2007, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res., 35, D61-5.
25. Warren, A.S., Archuleta, J., Feng, W.C. and Setubal, J.C. 2010, Missing genes in the annotation of prokaryotic genomes, BMC Bioinformatics, 11, 131.
26. Guo, F.B., Ou, H.Y. and Zhang, C.T. 2003, ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes, Nucleic Acids Res., 31, 1780-9.
27. Altschul, S.F., Wootton, J.C., Gertz, E.M., Agarwala, R., Morgulis, A., Schaffer, A.A. and Yu, Y.K. 2005, Protein database searches using compositionally adjusted substitution matrices, FEBS J., 272, 5101-9.
28. Zhang, C.T. and Wang, J. 2000, Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve, Nucleic Acids Res., 28, 2804-14.
29. Gao, N., Chen, L.L., Ji, H.F., et al. 2010, DIGA-a database of improved gene annotation for phytopathogens, BMC Genomics, 11, 54.
30. Gao, F. and Zhang, C.T. 2004, Comparison of various algorithms for recognizing short coding sequences of human genes, Bioinformatics, 20, 673-81.
31. Brazilian National Genome Project Consortium. 2003, The complete genome sequence of *Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability, Proc. Natl. Acad. Sci. USA, 100, 11660-5.
32. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W. and Hauser, L.J. 2010, Prodigal: prokaryotic gene recognition and translation initiation site identification, BMC Bioinformatics, 11, 119.
33. Richardson, E.J. and Watson, M. 2013, The automatic annotation of bacterial genomes, Brief Bioinform, 14, 1-12.
34. Salzberg, S.L. 2007, Genome re-annotation: a wiki solution? Genome Biol., 8, 102.
35. Zhang, C.T. and Chou, K.C. 1994, A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences, J. Mol. Biol., 238, 1-8.
36. Chen, L.L. and Zhang, C.T. 2003, Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages, Biochem. Biophys. Res. Commun., 306, 310-7.
37. Guo, F.B. 2007, The distribution patterns of bases of protein-coding genes, non-coding ORFs, and intergenic sequences in Pseudomonas aeruginosa PA01 genome and its implications, J. Biomol. Struct. Dyn., 25, 127-33.
38. Natale, D.A., Galperin, M.Y., Tatusovm, R.L. and Koonin, E.V. 2000, Using the COG database to improve gene recognition in complete genomes, Genetica, 108, 9-17.
39. Yu, J.F., Xiao, K., Jiang, D.K., Guo, J., Wang, J.H. and Sun, X. 2011, An integrative method for identifying the overannotated protein-coding genes in microbial genomes, DNA Res., 18, 435-49.
40. Luo, C., Hu, G.Q. and Zhu, H. 2009, Genome reannotation of Escherichia coli CFT073 with new insights into virulence, BMC Genomics, 10, 552.
41. Hayes, W.S. and Borodovsky, M. 1998, How to interpret an anonymous bacterial genome: machine learning approach to gene identification, Genome Res., 8, 1154-71.
42. Chung, G.T., Yoo, J.S., Oh, H.B., Lee, Y.S., Cha, S.H., Kim, S.J. and Yoo, C.K. 2008, Complete genome sequence of Neiserria gonorrhoeae NCCP11945, J. Bacteriol., 190, 6035-6.
43. Perrodou, E., Deshayes, C., Muller, J., et al. 2006, ICDS database: interrupted CoDing sequences in prokaryotic genomes, Nucleic Acids Res., 34, D338-43.
44. Sharma, V., Firth, A.E., Antonov, I., Fayet, O., Atkins, J.F., Borodovsky, M. and Baranov, P.V. 2011, A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment, Mol. Biol. Evol., 28, 3195-211.