Analyses of ORFans in microbial and viral genomes

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Analyses of ORFans in microbial and viral genomes

• Journal club presentation on Mar. 14
• Albert Yu

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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.)

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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

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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

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Classification of ORFans

• Singleton without any homolog wherever
• H1, BLASTP1
• Paralogous homologs in the same genome
• H1, BLASTPgt1
• Orthologous homologs within very closely related
  microbial genome
• Hgt1, U lt 0.1(by observations)

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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
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• 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

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

• Most OVH ltlt 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 ?????
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Viral genome
Microbial genome
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• 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)

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Some characteristics of ORFans

• Bacterial ORFans are shorter than non-ORFans on
  average
• Bacterial ORFans have significant lower GC3
  content than non-ORFans

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The length of Viral ORFans and non-ORFans
Length Non-ORFans gt ORFans
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Length ORFans lt non-ORFans
GC3 ORFans lt non-ORFans
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The number of ORFs per genome in 1456 viruses
Focusing on phage higher
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The growing of the number of phage ORFans
(consistent)
Keep increasing
38.4
Drop to 0 ?
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• 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)

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Less than 5 phages
Virus sampling bias between and within groups
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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
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the H-value percentages of phage ORFs
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• 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)