1、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 consideredNearly all genomes have ORFans (df %)The more genomes sequenced, the more ORFans have foundMost are
2、 annotated as hypothetical proteins of unknown function (no exp.),ORFan continue,More datareal , functional proteins3D nstructureconserved in closely related species (Ka/Ks),Origin of ORFans ?,Viral genome,Microbial genome,?,Viral laterally transferred genes (especially phages),Viral genome,Microbia
3、l genome,Question: the origin of ORFansTest hypothesis: ORFans have been acquired through lateral gene transfer from virusesTo find homologs to these microbial ORFans within the virus sequence database,Genome-wide quantitative study,BLASTP 277 microbial genomes 1456 viral genomes H(g): the number of
4、 genomes having at least one homolog of ORFan g U(g): uniqueness: the genomic distance between the genomes with ORFan g,Classification of ORFans,Singleton: without any homolog whereverH=1, BLASTP=1 Paralogous: homologs in the same genomeH=1, BLASTP1 Orthologous: homologs within very closely related
5、microbial genomeH1, U = 0.1(by observations),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%),0.64,S or p,O,ORFans-VH%(OVH): % of ORFans having homologs in viruses (0% 63.8%) Non-ORFans-VH%(NOVH): % of non-ORFans having
6、 homologs in viruses (4.1% 18.2%) The strength of the hypothesis = the value between these two VH%,Percentages of microbial ORFs with homologs in viruses,Red: OVH Blue: NOVH,24 phylogenetic clades,Bacteria,Archea,Firmicutes,Gamma proteobacteria,The average % of OVH and NOVH in various groups,148,66,
7、63,10% vs 9 %,8.5% vs 2.7 %,6.6% vs 0.8 %,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;
8、 69-others),Sampling ?,Viral genome,Microbial genome,277 Microbial genomes 1456 virusesAll-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),Some characteri
9、stics of ORFans,Bacterial ORFans are shorter than non-ORFans on averageBacterial ORFans have significant lower GC3 content than non-ORFans,The length of Viral ORFans and non-ORFans,Length: Non-ORFans ORFans,Length: ORFans non-ORFans,GC3%: ORFans non-ORFans,The number of ORFs per genome in 1456 virus
10、es,Focusing on phage: higher %,The growing of the number of phage ORFans (consistent),Drop to 0 ?,Keep increasing,38.4%,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 ph
11、age sampling),Less than 5 phages,Virus sampling bias between and within groups,The H-value percentages for all phage ORFs and prokaryotic ORFs,prokaryotes,phages,9.1% - ORFans,11.3% - ortho,38.4% - ORFans,32.4% - ortho,the H-value percentages of phage ORFs,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),
