Supporting Information Wu et al. 10.1073/pnas.0905115106 20 15 10 5 0 10 15 20 25 30 35 40 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. Wu et al. www.pnas.org/cgi/content/short/0905115106 1of6 20 18 16 14 12 10 8 6 0.0/0.5 0.5/0.7 0.7/0.9 0.9/1.1 1.1/1.3 1.3/1.5 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 NC࿝001493.1 Ictalurid herpesvirus 1 IcHV1 Alloherpesviridae unclassified NC࿝008210.1 Ranid herpesvirus 2 RaHV2 Alloherpesviridae unclassified NC࿝008211.1 Ranid herpesvirus 1 RaHV1 Alloherpesviridae unclassified NC࿝009127.1 Cyprinid herpesvirus 3 CyHV3 Ascoviridae Ascovirus NC࿝008361.1 Spodoptera frugiperda ascovirus SfAV-1a 1a Ascoviridae Ascovirus NC࿝008518.1 Trichoplusia ni ascovirus 2c TnAV-2c Ascoviridae Ascovirus NC࿝009233.1 Heliothis virescens ascovirus 3e HvAV-3e Asfarviridae Asfivirus NC࿝001659.1 African swine fever virus ASFV Baculoviridae Alphaabaculovirus NC࿝001623.1 Autographa californica AcMNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝001875.2 Orgyia pseudotsugata MNPV OpMNPV Baculoviridae Alphaabaculovirus NC࿝001962.1 Bombyx mori NPV BmNPV Baculoviridae Alphaabaculovirus NC࿝001973.1 Lymantria dispar MNPV LdMNPV Baculoviridae Alphaabaculovirus NC࿝002169.1 Spodoptera exigua MNPV SeMNPV Baculoviridae Alphaabaculovirus NC࿝002654.2 Helicoverpa armigera HearNPV-G4 nucleopolyhedrovirus G4 Baculoviridae Alphaabaculovirus NC࿝003083.1 Epiphyas postvittana NPV EppoNPV Baculoviridae Alphaabaculovirus NC࿝003094.2 Helicoverpa armigera NPV HearNPV-C1 Baculoviridae Alphaabaculovirus NC࿝003102.1 Spodoptera litura NPV SpltNPV Baculoviridae Alphaabaculovirus NC࿝003349.1 Helicoverpa zea SNPV HzSNPV Baculoviridae Alphaabaculovirus NC࿝003529.1 Mamestra configurata NPV-A MacoNPV-A Baculoviridae Alphaabaculovirus NC࿝004117.1 Mamestra configurata NPV-B MacoNPV-B Baculoviridae Alphaabaculovirus NC࿝004323.1 Rachiplusia ou MNPV RoMNPV Baculoviridae Alphaabaculovirus NC࿝004690.1 Adoxophyes honmai NPV AdhoNPV Baculoviridae Alphaabaculovirus NC࿝004778.3 Choristoneura fumiferana MNPV CfMNPV Baculoviridae Alphaabaculovirus NC࿝005137.2 Choristoneura fumiferana DEF CfDEFNPV MNPV Baculoviridae Alphaabaculovirus NC࿝007151.1 Chrysodeixis chalcites ChchNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝007383.1 Trichoplusia ni SNPV TnSNPV Baculoviridae Alphaabaculovirus NC࿝007767.1 Hyphantria cunea HycuNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝007921.1 Agrotis segetum AgseNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008035.3 Antheraea pernyi AnpeNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008293.1 Clanis bilineata ClbiNPV nucleopolyhedrosis virus Baculoviridae Alphaabaculovirus NC࿝008348.1 Leucania separata nuclear LeseNPV polyhedrosis virus Baculoviridae Alphaabaculovirus NC࿝008349.1 Plutella xylostella multiple PlxyMNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008520.1 Anticarsia gemmatalis AngeNPV nucleopolyhedrovirus Baculoviridae Alphaabaculovirus NC࿝008586.1 Ecotropis obliqua NPV EcobNPV Baculoviridae Alphaabaculovirus NC࿝008725.1 Maruca vitrata MNPV MaviMNPV Baculoviridae Alphaabaculovirus NC࿝009011.1 Spodoptera frugiperda MNPV SfMNPV Baculoviridae Alphaabaculovirus NC࿝010276.1 Orgyia leucostigma NPV OrleNPV Baculoviridae Betabaculovirus NC࿝002331.1 Xestia c-nigrum granulovirus XecnGV Baculoviridae Betabaculovirus NC࿝002593.1 Plutella xylostella granulovirus PlxyGV Baculoviridae Betabaculovirus NC࿝002816.1 Cydia pomonella granulovirus CpGV Baculoviridae Betabaculovirus NC࿝004062.1 Phthorimaea operculella PhopGV granulovirus Baculoviridae Betabaculovirus NC࿝005038.1 Adoxophyes orana granulovirus AdorGV Baculoviridae Betabaculovirus NC࿝005068.1 Cryptophlebia leucotreta CrleGV granulovirus Baculoviridae Betabaculovirus NC࿝005839.2 Agrotis segetum granulovirus AgseGV Baculoviridae Betabaculovirus NC࿝008168.1 Choristoneura occidentalis ChocGV granulovirus Baculoviridae Betabaculovirus NC࿝009503.1 Spodoptera litura granulovirus SpltGV Baculoviridae Betabaculovirus NC࿝010240.1 Helicoverpa armigera HearGV granulovirus Baculoviridae Deltabaculovirus NC࿝003084.1 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 NC࿝005905.1 Neodiprion sertifer NPV NeseNPV Baculoviridae Gammabaculovirus NC࿝005906.1 Neodiprion lecontii NPV NeleNPV Baculoviridae Gammabaculovirus NC࿝008252.1 Neodiprion abietis NeabNPV nucleopolyhedrovirus Herpesviridae Alphaherpesvirinae Iltovirus NC࿝005264.1 Psittacid herpesvirus 1 PsHV1 Herpesviridae Alphaherpesvirinae Iltovirus NC࿝006623.1 Gallid herpesvirus 1 GaHV1 Herpesviridae Alphaherpesvirinae Mardivirus NC࿝002229.3 Gallid herpesvirus 2 GaHV2 Herpesviridae Alphaherpesvirinae Mardivirus NC࿝002577.1 Gallid herpesvirus 3 GaHV3 Herpesviridae Alphaherpesvirinae Mardivirus NC࿝002641.1 Meleagrid herpesvirus 1 MeHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝001798.1 Human herpesvirus 2 HHV2 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝001806.1 Human herpesvirus 1 HHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝004812.1 Macacine herpesvirus 1 MaHV1 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝006560.1 Cercopithecine herpesvirus 2 CeHV2 Herpesviridae Alphaherpesvirinae Simplexvirus NC࿝007653.1 Papiine herpesvirus 2 PaHV2 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001348.1 Human herpesvirus 3 HHV3 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001491.2 Equid herpesvirus 1 EHV1 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001844.1 Equid herpesvirus 4 EHV4 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝001847.1 Bovine herpesvirus 1 BHV1 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝002686.2 Cercopithecine herpesvirus 9 CeHV9 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝005261.2 Bovine herpesvirus 5 BHV5 Herpesviridae Alphaherpesvirinae Varicellovirus NC࿝006151.1 Suid herpesvirus 1 SuHV1 Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝001347.3 Human herpesvirus 5 strain HHV5-AD169 AD169 Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝003521.1 Panine herpesvirus 2 CCMV Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝006150.1 Macacine herpesvirus 8 MaHV8 Herpesviridae Betaherpesvirinae Cytomegalovirus NC࿝006273.2 Human herpesvirus 5 HHV5 Herpesviridae Betaherpesvirinae Muromegalovirus NC࿝002512.2 Murid herpesvirus 2 MHV2 Herpesviridae Betaherpesvirinae Muromegalovirus NC࿝004065.1 Murid herpesvirus 1 MHV1 Herpesviridae Betaherpesvirinae Roseolovirus NC࿝000898.1 Human herpesvirus 6B HHV6B Herpesviridae Betaherpesvirinae Roseolovirus NC࿝001664.1 Human herpesvirus 6A HHV6A Herpesviridae Betaherpesvirinae Roseolovirus NC࿝001716.2 Human herpesvirus 7 HHV7 Herpesviridae Betaherpesvirinae unclassified NC࿝002794.1 Tupaiid herpesvirus 1 TuHV1 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝004367.1 Callitrichine herpesvirus 3 CalHV3 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝006146.1 Macacine herpesvirus 4 MaHV4 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝007605.1 Human herpesvirus 4 type 1 HHV4–1 Herpesviridae Gammaherpesvirinae Lymphocryptovirus NC࿝009334.1 Human herpesvirus 4 type 2 HHV4–2 Herpesviridae Gammaherpesvirinae Macavirus NC࿝002531.1 Alcelaphine herpesvirus 1 AHV1 Herpesviridae Gammaherpesvirinae Macavirus NC࿝007646.1 Ovine herpesvirus 2 OHV2 Herpesviridae Gammaherpesvirinae Percavirus NC࿝001650.1 Equid herpesvirus 2 EHV2 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝001350.1 Saimiriine herpesvirus 2 SaHV2 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝001826.2 Murid herpesvirus 4 MHV4 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝001987.1 Ateline herpesvirus 3 AtHV3 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝002665.1 Bovine herpesvirus 4 BHV4 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝003401.1 Macacine herpesvirus 5 MaHV5 Herpesviridae Gammaherpesvirinae Rhadinovirus NC࿝003409.1 Human herpesvirus