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Analyses of ORFans in microbial and viral genomes

Analyses of ORFans in microbial and viral genomes. Journal club presentation on Mar. 14 Albert Yu. ORFan. Defenition: an ORF with no detectable sequence similarity to other ORFs in the database considered Nearly all genomes have ORFans (df %)

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Analyses of ORFans in microbial and viral genomes

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  1. Analyses of ORFans in microbial and viral genomes Journal club presentation on Mar. 14 Albert Yu

  2. ORFan Defenition: an ORF with no detectable sequence similarity to other ORFs in the database considered Nearly all genomes have ORFans (df %) The more genomes sequenced, the more ORFans have found Most are annotated as hypothetical proteins of unknown function (no exp.)

  3. ORFan continue More data… real , functional proteins 3D nstructure conserved in closely related species (Ka/Ks) Origin of ORFans ???????? Viral laterally transferred genes (especially phages) ? Viral genome Microbial genome

  4. Viral genome Microbial genome

  5. Question: the origin of ORFans Test hypothesis: ORFans have been acquired through lateral gene transfer from viruses To find homologs to these microbial ORFans within the virus sequence database

  6. Genome-wide quantitative study • BLASTP • 277 microbial genomes • 1456 viral genomes • H(g): the number of genomes having at least one homolog of ORFan g • U(g): uniqueness: the genomic distance between the genomes with ORFan g

  7. Classification of ORFans • Singleton: without any homolog wherever H=1, BLASTP=1 • Paralogous: homologs in the same genome H=1, BLASTP>1 • Orthologous: homologs within very closely related microbial genome H>1, U <= 0.1(by observations)

  8. The U-value for all ORFs in prokaryote genomes In total: ORFs: 818906 ORFans: 110186 S: 64324(7.8%) P: 10419(1.3%) O: 35443(4.3%) S or p 0.64 O

  9. ORFans-VH%(OVH): % of ORFans having homologs in viruses (0% ~ 63.8%) • Non-ORFans-VH%(NOVH): % of non-ORFans having homologs in viruses (4.1% ~ 18.2%) • The strength of the hypothesis = the value between these two VH%

  10. Percentages of microbial ORFs with homologs in viruses Gamma proteobacteria Red: OVH Blue: NOVH 24 phylogenetic clades Bacteria Firmicutes Archea

  11. The average % of OVH and NOVH in various groups 6.6% vs 0.8 % 148 10% vs 9 % 63 8.5% vs 2.7 % 66

  12. Conclusion • Most OVH << NOVH: current evidence supporting the hypothesis is weak • Firmicutes and Gamma-proteobacteria have the highest number of homologs in viruses (viral database is biased) Viral database bias 1456 viruses 280 phages (109--Gamma; 102--Firmicutes; 69--others) Sampling ?????

  13. Viral genome Microbial genome

  14. 277 Microbial genomes • 1456 viruses All-virus-DB: 43566 ORFs • 280 phages (20%) Phage-DB: 18368 ORFs (42%) ORFans: all-virus: 13078(30%) (v.s. all-virus-DB) 8200 (v.s. all nr, env-nr) all-phage: 6765 (v.s. all-virus-DB) 7047 (v.s. phage-DB)

  15. Some characteristics of ORFans • Bacterial ORFans are shorter than non-ORFans on average • Bacterial ORFans have significant lower GC3 content than non-ORFans

  16. The length of Viral ORFans and non-ORFans Length: Non-ORFans > ORFans

  17. Length: ORFans < non-ORFans GC3%: ORFans < non-ORFans

  18. The number of ORFs per genome in 1456 viruses Focusing on phage: higher %

  19. The growing of the number of phage ORFans (consistent) Keep increasing 38.4% Drop to 0 ?

  20. Each microbial species is a host for at least 10 phage species --- the phage diversity is at least 10 times higher than microbial diversity • Only 280 phage genomes in database (low phage sampling)

  21. Less than 5 phages Virus sampling bias between and within groups

  22. The H-value percentages for all phage ORFs and prokaryotic ORFs prokaryotes phages 38.4% - ORFans 9.1% - ORFans 32.4% - ortho 11.3% - ortho

  23. the H-value percentages of phage ORFs

  24. 4397(61.5%) / 7150(63.8%) / 11212 (prophage/ prokaryotic homologs/ phage non-ORFans) • 589(44.7%) / 1317(18.7%) / 7047 (prophage/ prokaryotic homologs/ phage ORFans) • 4987(58.9%)/8467(46.4%)/18248 (prophage/ prokaryotic homologs/ phage ORFs)

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