Detection of atypical genes in virus families using a one-class SVM

BMC Genomics

Olga V Kalinina¹  Saskia Metzler¹ 

[1]Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany

关键词: SVM;    Machine learning;    Viral evolution;    Horizontal gene transfer;   

Others  :  1128443
DOI  :  10.1186/1471-2164-15-913

 received in 2014-08-13, accepted in 2014-10-10,  发布年份 2014

【 摘 要 】

Background

The diversity of viruses, the absence of universally common genes in them, and their ability to act as carriers of genetic material make assessment of evolutionary paths of viral genes very difficult. One important factor contributing to this complexity is horizontal gene transfer.

Results

We explore the possibility for the systematic identification of atypical genes within virus families, including viruses whose genome is not encoded by a double-stranded DNA. Our method is based on gene statistical features that differ in genes that were subject of recent horizontal gene transfer from those of the genome in which they are observed. We employ a one-class SVM approach to detect atypical genes within a virus family basing of their statistical signatures and without explicit knowledge of the source species. The simplicity of the statistical features used makes the method applicable to various viruses irrespective of their genome size or type.

Conclusions

On simulated data, the method can robustly identify alien genes irrespective of the coding nucleic acid found in a virus. It also compares well to results obtained in related studies for double-stranded DNA viruses. Its value in practice is confirmed by the identification of isolated examples of horizontal gene transfer events that have already been described in the literature. A Python package implementing the method and the results for the analyzed virus families are available at http://svm-agp.bioinf.mpi-inf.mpg.de webcite.

【 授权许可】

   
2014 Metzler and Kalinina; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

【 参考文献 】

• [1]Koonin EV, Senkevich TG, Dolja VV: Compelling reasons why viruses are relevant for the origin of cells. Nat Rev Microbiol 2009, 7(8):615.
• [2]Syvanen M: Evolutionary implications of horizontal gene transfer. Annu Rev Genet 2012, 46(1):341-358.
• [3]Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55:709-742.
• [4]Dimmock N, Easton A, Leppard K: Introduction to Modern Virology. Oxford: Blackwell Science; 2009.
• [5]Lawrence JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44(4):383-397.
• [6]Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW: Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol 2006, 4(8):234.
• [7]Monier A, Pagarete A, de Vargas C, Allen MJ, Read B, Claverie J-M, Ogata H: Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res 2009, 19(8):1441-1449.
• [8]Schoenfeld TW, Murugapiran SK, Dodsworth JA, Floyd S, Lodes M, Mead DA, Hedlund BP: Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa. Mol Biol Evol 2013, 30(7):1653-1664.
• [9]Odom MR, Hendrickson RC, Lefkowitz EJ: Poxvirus protein evolution: family wide assessment of possible horizontal gene transfer events. Virus Res 2009, 144(1–2):233-249.
• [10]La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin EV, Raoult D: The virophage as a unique parasite of the giant mimivirus. Nature 2008, 455(7209):100-104.
• [11]Claverie J-M, Abergel C: Mimivirus and its virophage. Annu Rev Genet 2009, 43:49-66.
• [12]Becq J, Churlaud C, Deschavanne P: A benchmark of parametric methods for horizontal transfers detection. PLoS ONE 2010, 5(4):9989.
• [13]Tsirigos A, Rigoutsos I: A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Res 2005, 33(12):3699-3707.
• [14]Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F: The marine viromes of four oceanic regions. PLoS Biol 2006, 4:368.
• [15]Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB: Metagenomic and small-subunit rrna analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 2007, 73(21):7059-7066.
• [16]Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, Wang D: Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 2008, 4(2):1000011.
• [17]Schölkopf B, Williamson R, Smola A, Shawe-Taylor J, Platt J: Support vector method for novelty detection. In NIPS. Edited by Solla SA, Leen TK, Müller K-R. Cambridge: MIT Press; 2000:582-588.
• [18]Tax D: One-class classification Concept-learning in the absence of counter-examples. Dissertation, Technische Universiteit Delft; 2001.
• [19]King AMQ, Lefkowitz E, Adams MJ, Carstens EB: Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Kidlington: Elsevier Science; 2011. Immunology and Microbiology; 2011.
• [20]Lawrence JG, Ochman H: Molecular archaeology of the escherichia coli genome. Proc Natl Acad Sci U S A 1998, 95(16):9413-9417.
• [21]Daubin V, Lerat E, Perrière G: The source of laterally transferred genes in bacterial genomes. Genome Biol 2003, 4(9):57. BioMed Central Full Text
• [22]Zhu W, Lomsadze A, Borodovsky M: Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 2010, 38(12):132.
• [23]Zwillinger D, Kokoska S: CRC Standard Probability and Statistics Tables and Formulae. London: CRC Press; 2010.
• [24]Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G: The European nucleotide archive. Nucleic Acids Res 2011, 39(Database issue):28-31.
• [25]Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658-1659.
• [26]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
• [27]Magrane M, Consortium U: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011, 2011:009.
• [28]Zamenhof S, Chargaff E, Braverman G: Dissymmetry in nucleotide sequence of desoxypentose nucleic acids. J Biol Chem 1950, 187(1):1-14.
• [29]Rudner R, Karkas JD, Chargaff E: Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc Natl Acad Sci U S A 1968, 60(3):921-922.
• [30]Nobusawa E, Sato K: Comparison of the mutation rates of human influenza A and B viruses. J Virol 2006, 80(7):3675-3678.
• [31]Morse M, Marriott A, Nuttall P: The glycoprotein of Thogoto virus (a tick-borne orthomyxo-like virus) is related to the baculovirus glycoprotein GP64. Virology 1992, 186(2):640-646.
• [32]Meehan BM, Creelan JL, McNulty MS, Todd D: Sequence of porcine circovirus DNA: affinities with plant circoviruses. J Gen Virol 1997, 78(Pt 1):221-227.
• [33]Gibbs MJ, Smeianov VV, Steele JL, Upcroft P, Efimov BA: Two families of rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes. Mol Biol Evol 2006, 23(6):1097-1100.
• [34]Mitsuyoshi Y, Sumiko N, Naotake O, Hiroshi Y: Integration of woodchuck hepatitis virus (WHY) DNA at two chromosomal sites (Vk andgag-like) in a hepatocellular carcinoma. Gene 1991, 100:139-146.
• [35]Liu W, Pan S, Yang H, Bai W, Shen Z, Liu J, Xie Y: The first full-length endogenous hepadnaviruses: identification and analysis. J Virol 2012, 86(17):9510-9513.
• [36]Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P: Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res 2005, 33(1):6.
• [37]Hughes AL, Irausquin S, Friedman R: The evolutionary biology of poxviruses. Infect Genet Evol 2010, 10(1):50-59.
• [38]Filée J, Pouget N, Chandler M: Phylogenetic evidence for extensive lateral acquisition of cellular genes by nucleocytoplasmic large DNA viruses. BMC Evol Biol 2008, 8:320. BioMed Central Full Text