Supporting Information
Wu et al. 10.1073/pnas.0905115106
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Fig. S1. HGT cutoff and tree topology. Robinson-Foulds (RF) distance [Robinson DF, Foulds LR (1981) Math Biosci 53:131–147] between viral proteome trees with different horizontal gene transfer (HGT) cutoffs h at feature length 8. Tree distances are between h and h-1. The tree topology remains stable for h in the range 13–31. We use h ϭ 20 in this work.
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Fig. S2. Low complexity features and tree topology. Robinson-Foulds (RF) distance between viral proteome trees with different low-complexity cutoffs K2 for feature length 8 and HGT cutoff 20. The tree topology changes least for K2 ϭ 0.9, 1.1 and 1.3. We choose K2 ϭ 1.1 for this study.
Wu et al. www.pnas.org/cgi/content/short/0905115106 2of6 Table S1. Distribution of the 164 inter-viral-family HGT instances bro hr RR2 RR1 IL-10 Ubi TS Photol. Total
Baculo 45 1 10 9 11 1 77 Asco 11 7 1 19 Nudi 1 1 1 3 SGHV 1 1 2 Nima 1 1 2 Herpes 48 12 Pox 18 8 2 3 1 3 35 Irido 1 1 2 4 Phyco 2 3 2 1 8 Allo 1 1 2 Total 56 8 35 24 6 17 14 4 164
The HGT cutoff is 20 8-mers. These HGT instances involve 8 gene families: baculovirus repeated ORF (bro), homologous region (hr), ribonucleotide reductase large subunit (RR1) and small subunit (RR2), interleukin 10 (IL-10), ubiquitin (Ubi), thymidylate synthase (TS), DNA photolyase 2 (photol). The involved viral families are: baculoviridae (Baculo), ascoviridae (Asco) nudivirus (Nudi), saliva gland hypertrophy virus (SGHV), nimaviridae (Nima), herpesviridae (Herpes), poxviridae (Pox), iridoviridae (Irido), phycodnaviridae (Phyco), alloherpesviridae (Allo).
Wu et al. www.pnas.org/cgi/content/short/0905115106 3of6 Table S2. List of 142 large dsDNA viruses Family Subfamily Genus NCBI Accession Code Virus name Abbreviation
Alloherpesviridae Ictalurivirus NC001493.1 Ictalurid herpesvirus 1 IcHV1 Alloherpesviridae unclassified NC008210.1 Ranid herpesvirus 2 RaHV2 Alloherpesviridae unclassified NC008211.1 Ranid herpesvirus 1 RaHV1 Alloherpesviridae unclassified NC009127.1 Cyprinid herpesvirus 3 CyHV3 Ascoviridae Ascovirus NC008361.1 Spodoptera frugiperda ascovirus SfAV-1a 1a Ascoviridae Ascovirus NC008518.1 Trichoplusia ni ascovirus 2c TnAV-2c Ascoviridae Ascovirus NC009233.1 Heliothis virescens ascovirus 3e HvAV-3e Asfarviridae Asfivirus NC001659.1 African swine fever virus ASFV Baculoviridae Alphaabaculovirus NC001623.1 Autographa californica AcMNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC001875.2 Orgyia pseudotsugata MNPV OpMNPV Baculoviridae Alphaabaculovirus NC001962.1 Bombyx mori NPV BmNPV Baculoviridae Alphaabaculovirus NC001973.1 Lymantria dispar MNPV LdMNPV Baculoviridae Alphaabaculovirus NC002169.1 Spodoptera exigua MNPV SeMNPV Baculoviridae Alphaabaculovirus NC002654.2 Helicoverpa armigera HearNPV-G4 nucleopolyhedrovirus G4 Baculoviridae Alphaabaculovirus NC003083.1 Epiphyas postvittana NPV EppoNPV Baculoviridae Alphaabaculovirus NC003094.2 Helicoverpa armigera NPV HearNPV-C1 Baculoviridae Alphaabaculovirus NC003102.1 Spodoptera litura NPV SpltNPV Baculoviridae Alphaabaculovirus NC003349.1 Helicoverpa zea SNPV HzSNPV Baculoviridae Alphaabaculovirus NC003529.1 Mamestra configurata NPV-A MacoNPV-A Baculoviridae Alphaabaculovirus NC004117.1 Mamestra configurata NPV-B MacoNPV-B Baculoviridae Alphaabaculovirus NC004323.1 Rachiplusia ou MNPV RoMNPV Baculoviridae Alphaabaculovirus NC004690.1 Adoxophyes honmai NPV AdhoNPV Baculoviridae Alphaabaculovirus NC004778.3 Choristoneura fumiferana MNPV CfMNPV Baculoviridae Alphaabaculovirus NC005137.2 Choristoneura fumiferana DEF CfDEFNPV MNPV Baculoviridae Alphaabaculovirus NC007151.1 Chrysodeixis chalcites ChchNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC007383.1 Trichoplusia ni SNPV TnSNPV Baculoviridae Alphaabaculovirus NC007767.1 Hyphantria cunea HycuNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC007921.1 Agrotis segetum AgseNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC008035.3 Antheraea pernyi AnpeNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC008293.1 Clanis bilineata ClbiNPV nucleopolyhedrosis virus Baculoviridae Alphaabaculovirus NC008348.1 Leucania separata nuclear LeseNPV polyhedrosis virus Baculoviridae Alphaabaculovirus NC008349.1 Plutella xylostella multiple PlxyMNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC008520.1 Anticarsia gemmatalis AngeNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC008586.1 Ecotropis obliqua NPV EcobNPV Baculoviridae Alphaabaculovirus NC008725.1 Maruca vitrata MNPV MaviMNPV Baculoviridae Alphaabaculovirus NC009011.1 Spodoptera frugiperda MNPV SfMNPV Baculoviridae Alphaabaculovirus NC010276.1 Orgyia leucostigma NPV OrleNPV Baculoviridae Betabaculovirus NC002331.1 Xestia c-nigrum granulovirus XecnGV Baculoviridae Betabaculovirus NC002593.1 Plutella xylostella granulovirus PlxyGV Baculoviridae Betabaculovirus NC002816.1 Cydia pomonella granulovirus CpGV Baculoviridae Betabaculovirus NC004062.1 Phthorimaea operculella PhopGV granulovirus Baculoviridae Betabaculovirus NC005038.1 Adoxophyes orana granulovirus AdorGV Baculoviridae Betabaculovirus NC005068.1 Cryptophlebia leucotreta CrleGV granulovirus Baculoviridae Betabaculovirus NC005839.2 Agrotis segetum granulovirus AgseGV Baculoviridae Betabaculovirus NC008168.1 Choristoneura occidentalis ChocGV granulovirus Baculoviridae Betabaculovirus NC009503.1 Spodoptera litura granulovirus SpltGV Baculoviridae Betabaculovirus NC010240.1 Helicoverpa armigera HearGV granulovirus Baculoviridae Deltabaculovirus NC003084.1 Culex nigripalpus NPV CuniNPV
Wu et al. www.pnas.org/cgi/content/short/0905115106 4of6 Family Subfamily Genus NCBI Accession Code Virus name Abbreviation
Baculoviridae Gammabaculovirus NC005905.1 Neodiprion sertifer NPV NeseNPV Baculoviridae Gammabaculovirus NC005906.1 Neodiprion lecontii NPV NeleNPV Baculoviridae Gammabaculovirus NC008252.1 Neodiprion abietis NeabNPV nucleopolyhedrovirus Herpesviridae Alphaherpesvirinae Iltovirus NC005264.1 Psittacid herpesvirus 1 PsHV1 Herpesviridae Alphaherpesvirinae Iltovirus NC006623.1 Gallid herpesvirus 1 GaHV1 Herpesviridae Alphaherpesvirinae Mardivirus NC002229.3 Gallid herpesvirus 2 GaHV2 Herpesviridae Alphaherpesvirinae Mardivirus NC002577.1 Gallid herpesvirus 3 GaHV3 Herpesviridae Alphaherpesvirinae Mardivirus NC002641.1 Meleagrid herpesvirus 1 MeHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC001798.1 Human herpesvirus 2 HHV2 Herpesviridae Alphaherpesvirinae Simplexvirus NC001806.1 Human herpesvirus 1 HHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC004812.1 Macacine herpesvirus 1 MaHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC006560.1 Cercopithecine herpesvirus 2 CeHV2 Herpesviridae Alphaherpesvirinae Simplexvirus NC007653.1 Papiine herpesvirus 2 PaHV2 Herpesviridae Alphaherpesvirinae Varicellovirus NC001348.1 Human herpesvirus 3 HHV3 Herpesviridae Alphaherpesvirinae Varicellovirus NC001491.2 Equid herpesvirus 1 EHV1 Herpesviridae Alphaherpesvirinae Varicellovirus NC001844.1 Equid herpesvirus 4 EHV4 Herpesviridae Alphaherpesvirinae Varicellovirus NC001847.1 Bovine herpesvirus 1 BHV1 Herpesviridae Alphaherpesvirinae Varicellovirus NC002686.2 Cercopithecine herpesvirus 9 CeHV9 Herpesviridae Alphaherpesvirinae Varicellovirus NC005261.2 Bovine herpesvirus 5 BHV5 Herpesviridae Alphaherpesvirinae Varicellovirus NC006151.1 Suid herpesvirus 1 SuHV1 Herpesviridae Betaherpesvirinae Cytomegalovirus NC001347.3 Human herpesvirus 5 strain HHV5-AD169 AD169 Herpesviridae Betaherpesvirinae Cytomegalovirus NC003521.1 Panine herpesvirus 2 CCMV Herpesviridae Betaherpesvirinae Cytomegalovirus NC006150.1 Macacine herpesvirus 8 MaHV8 Herpesviridae Betaherpesvirinae Cytomegalovirus NC006273.2 Human herpesvirus 5 HHV5 Herpesviridae Betaherpesvirinae Muromegalovirus NC002512.2 Murid herpesvirus 2 MHV2 Herpesviridae Betaherpesvirinae Muromegalovirus NC004065.1 Murid herpesvirus 1 MHV1 Herpesviridae Betaherpesvirinae Roseolovirus NC000898.1 Human herpesvirus 6B HHV6B Herpesviridae Betaherpesvirinae Roseolovirus NC001664.1 Human herpesvirus 6A HHV6A Herpesviridae Betaherpesvirinae Roseolovirus NC001716.2 Human herpesvirus 7 HHV7 Herpesviridae Betaherpesvirinae unclassified NC002794.1 Tupaiid herpesvirus 1 TuHV1 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC004367.1 Callitrichine herpesvirus 3 CalHV3 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC006146.1 Macacine herpesvirus 4 MaHV4 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC007605.1 Human herpesvirus 4 type 1 HHV4–1 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC009334.1 Human herpesvirus 4 type 2 HHV4–2 Herpesviridae Gammaherpesvirinae Macavirus NC002531.1 Alcelaphine herpesvirus 1 AHV1 Herpesviridae Gammaherpesvirinae Macavirus NC007646.1 Ovine herpesvirus 2 OHV2 Herpesviridae Gammaherpesvirinae Percavirus NC001650.1 Equid herpesvirus 2 EHV2 Herpesviridae Gammaherpesvirinae Rhadinovirus NC001350.1 Saimiriine herpesvirus 2 SaHV2 Herpesviridae Gammaherpesvirinae Rhadinovirus NC001826.2 Murid herpesvirus 4 MHV4 Herpesviridae Gammaherpesvirinae Rhadinovirus NC001987.1 Ateline herpesvirus 3 AtHV3 Herpesviridae Gammaherpesvirinae Rhadinovirus NC002665.1 Bovine herpesvirus 4 BHV4 Herpesviridae Gammaherpesvirinae Rhadinovirus NC003401.1 Macacine herpesvirus 5 MaHV5 Herpesviridae Gammaherpesvirinae Rhadinovirus NC003409.1 Human herpesvirus 8 type M HHV8-M Herpesviridae Gammaherpesvirinae Rhadinovirus NC007016.1 Macaca fuscata rhadinovirus MafuHV Herpesviridae Gammaherpesvirinae Rhadinovirus NC009333.1 Human herpesvirus 8 type P HHV8-P Iridoviridae Chloriridovirus NC008187.1 Invertebrate iridescent virus 3 IIV3 Iridoviridae Iridovirus NC003038.1 Invertebrate iridescent virus 6 IIV6 Iridoviridae Lymphocystivirus NC001824.1 Lymphocystis disease virus 1 LCDV1 Iridoviridae Lymphocystivirus NC005902.1 Lymphocystis disease virus - LCDV-C isolate China Iridoviridae Megalocytivirus NC003494.1 Infectious spleen and kidney ISKNV necrosis virus Iridoviridae Ranavirus NC005832.1 Ambystoma tigrinum virus ATV Iridoviridae Ranavirus NC005946.1 Frog virus 3 FV3 Iridoviridae Ranavirus NC006549.1 Singapore grouper iridovirus SGIV Malacoherpesviridae Ostreavirus NC005881.1 Ostreid herpesvirus 1 OsHV-1 Mimiviridae Mimivirus NC006450.1 Acanthamoeba polyphaga APMV mimivirus Nimaviridae Whispovirus NC003225.1 Shrimp white spot syndrome WSSV virus Phycodnaviridae Chlorovirus NC000852.4 Paramecium bursaria Chlorella PBCV1 virus 1
Wu et al. www.pnas.org/cgi/content/short/0905115106 5of6 Family Subfamily Genus NCBI Accession Code Virus name Abbreviation
Phycodnaviridae Chlorovirus NC008603.1 Paramecium bursaria Chlorella PBCV-FR483 virus FR483 Phycodnaviridae Chlorovirus NC008724.1 Acanthocystis turfacea Chlorella ATCV-1 virus 1 Phycodnaviridae Chlorovirus NC009898.1 Paramecium bursaria Chlorella PBCV-NY2A virus NY2A Phycodnaviridae Chlorovirus NC009899.1 Paramecium bursaria Chlorella PBCV-AR158 virus AR158 Phycodnaviridae Coccolithovirus NC007346.1 Emiliania huxleyi virus 86 EhV-86 Phycodnaviridae Phaeovirus NC002687.1 Ectocarpus siliculosus virus 1 EsV Phycodnaviridae Phaeovirus NC011183.1 Feldmannia species virus FsV Phycodnaviridae Prasinovirus NC010191.1 Ostreococcus virus OsV5 OtV5 Poxviridae Chordopoxvirinae Avipoxvirus NC002188.1 Fowlpox virus FWPV Poxviridae Chordopoxvirinae Avipoxvirus NC005309.1 Canarypox virus CNPV Poxviridae Chordopoxvirinae Capripoxvirus NC003027.1 Lumpy skin disease virus NI-2490 LSDV Poxviridae Chordopoxvirinae Capripoxvirus NC004002.1 Sheeppox virus SHPV Poxviridae Chordopoxvirinae Capripoxvirus NC004003.1 Goatpox virus Pellor GTPV Poxviridae Chordopoxvirinae Cervidpoxvirus NC006966.1 Mule deer poxvirus DPV Poxviridae Chordopoxvirinae Leporipoxvirus NC001132.2 Myxoma virus MYXV Poxviridae Chordopoxvirinae Leporipoxvirus NC001266.1 Rabbit fibroma virus SHFV Poxviridae Chordopoxvirinae Molluscipoxvirus NC001731.1 Molluscum contagiosum virus MOCV Poxviridae Chordopoxvirinae Orthopoxvirus NC001611.1 Variola virus VARV Poxviridae Chordopoxvirinae Orthopoxvirus NC003310.1 Monkeypox virus MPV Poxviridae Chordopoxvirinae Orthopoxvirus NC003391.1 Camelpox virus CMPV Poxviridae Chordopoxvirinae Orthopoxvirus NC003663.2 Cowpox virus CPV Poxviridae Chordopoxvirinae Orthopoxvirus NC004105.1 Ectromelia virus ECTV Poxviridae Chordopoxvirinae Orthopoxvirus NC006998.1 Vaccinia virus VACV Poxviridae Chordopoxvirinae Orthopoxvirus NC008291.1 Taterapox virus TATV Poxviridae Chordopoxvirinae Parapoxvirus NC005336.1 Orf virus ORFV Poxviridae Chordopoxvirinae Parapoxvirus NC005337.1 Bovine papular stomatitis virus BPSV Poxviridae Chordopoxvirinae Suipoxvirus NC003389.1 Swinepox virus SWPV Poxviridae Chordopoxvirinae Yatapoxvirus NC002642.1 Yaba-like disease virus YLDV Poxviridae Chordopoxvirinae Yatapoxvirus NC005179.1 Yaba monkey tumor virus YMTV Poxviridae Chordopoxvirinae Yatapoxvirus NC009888.1 Tanapox virus TPV Poxviridae Chordopoxvirinae unclassified NC008030.1 Crocodilepox virus CRV Poxviridae Entomopoxvirinae Betaentomopoxvirus NC002520.1 Amsacta moorei AmEPV entomopoxvirus L Poxviridae Entomopoxvirinae unclassified NC001993.1 Melanoplus sanguinipes MsEPV entomopoxvirus Unclassified Nudivirus NC004156.1 Heliothis zea virus 1 HzNV-1 Unclassified Nudivirus NC009240.1 Gryllus bimaculatus nudivirus GbNV Unclassified unclassified NC010356.1 Glossina pallidipes salivary gland GpSGHV hypertrophy virus Unclassified unclassified NC010671.1 Musca domestica salivary gland MdSGHV hypertrophy virus
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