1 Fig S1: Genome organization of known viruses in Togaviridae (A) Non-structural Structural polyprotein polyprotein 59 nt (2,514 aa) (1,246 aa) 319 nt Sindbis virus (11,703 nt) 5’ Met Hel RdRp -E1 3’ (Genus Alphavirus) (B) Non-structural Structural polyprotein polyprotein 40 nt(2,117 aa) (1,064aa) 59 nt Rubella virus (Genus Rubivirus) 2 (9,762 nt) 5’ Hel RdRp Rubella_E1 3’ 3 4 Genome organization of known viruses in Togaviridae; (A) Sindbis virus and (B) Rubella virus. 5 Domains: Met, Vmethyltransf super family; Hel, Viral_helicase1 super family; RdRp, RdRP_2 6 super family; -E1, Alpha_E1_glycop super family; Rubella E1, Rubella membrane 7 glycoprotein E1. 8 9 Table S1: Origins of the FLDS reads reads ratio (%) trimmed reads 134513 100.0 OjRV 125004* 92.9 Cell 1001** 0.7 Eukcariota 749 Osedax 153 Symbiodinium 35 Spironucleus 15 Others 546 Bacteria 246 Not assigned 6 Not assigned 59** 0.0 No hit 8449** 6.2 10 *: Count of mapped reads on the OjRV genome sequence. 1 11 **: Homology search was performed using Blastn and Blastx, and the results were assigned by 12 MEGAN (6). 13 14 Table S2: Blastp hit list of predicted ORF1. Database virus protein accession e-value family non-redundant Ross River virus nsP4 protein NP_740681 2.00E-55 Togaviridae protein sequences non-redundant Getah virus nonstructural ARK36627 2.00E-50 Togaviridae protein polyprotein sequences non-redundant Sagiyama virus polyprotein BAA92845 2.00E-50 Togaviridae protein sequences non-redundant Alphavirus M1 nsp1234 ABK32031 3.00E-50 Togaviridae protein sequences non-redundant Mayaro virus Nsp4 ALI88625 8.00E-50 Togaviridae protein sequences non-redundant Middelburg virus nonstructural AAA96653 1.00E-49 Togaviridae protein polyprotein sequences non-redundant Semliki forest putative CAA75053 2.00E-49 Togaviridae protein virus RNA-dependent RNA sequences polymerase non-redundant Chikungunya virus non-structural ADZ04935 2.00E-48 Togaviridae protein polyprotein sequences non-redundant Bebaru virus non-structural YP_008901140 2.00E-48 Togaviridae protein polyprotein precursor sequences nsP1234 non-redundant O'nyong-nyong nonstructural protein NP_740706 5.00E-48 Togaviridae protein virus P4 sequences non-redundant Sleeping disease non structural protein NP_740656 5.00E-48 Togaviridae protein virus P4 2 sequences NCBI Protein Ross River virus nsP4 protein NP_740681 1.00E-55 Togaviridae Reference Sequences NCBI Protein Getah virus nsP1234 polyprotein YP_164438 9.00E-50 Togaviridae Reference Sequences NCBI Protein Semliki Forest nonstructural protein NP_740668 1.00E-49 Togaviridae Reference virus nsP4 Sequences NCBI Protein Mayaro virus nonstructural protein NP_740690 3.00E-49 Togaviridae Reference nsP4 Sequences NCBI Protein Middelburg virus non-structural YP_009058892 1.00E-48 Togaviridae Reference polyprotein Sequences NCBI Protein Bebaru virus non-structural YP_008901140 1.00E-48 Togaviridae Reference polyprotein precursor Sequences nsP1234 NCBI Protein O'nyong-nyong nonstructural protein NP_740706 3.00E-48 Togaviridae Reference virus P4 Sequences NCBI Protein Sleeping disease non structural protein NP_740656 4.00E-48 Togaviridae Reference virus P4 Sequences NCBI Protein Chikungunya virus nonstructural NP_690588 3.00E-47 Togaviridae Reference polyprotein Sequences NCBI Protein Ndumu virus non-structural YP_008888544 1.00E-46 Togaviridae Reference polyprotein precursor Sequences nsP1234 NCBI Protein Fort Morgan virus nsP4 YP_003324594 4.00E-46 Togaviridae Reference Sequences NCBI Protein Sindbis virus nsp4 nonstructural NP_740669 8.00E-46 Togaviridae Reference protein Sequences NCBI Protein Salmon pancreas non structural protein NP_740638 4.00E-45 Togaviridae Reference disease virus P4 Sequences 3 NCBI Protein Tai Forest non-structural YP_009333615 7.00E-45 Togaviridae Reference alphavirus polyprotein Sequences NCBI Protein Madariaga virus RNA-directed RNA YP_009020586 4.00E-44 Togaviridae Reference polymerase nsp4 Sequences NCBI Protein Barmah Forest non-structural NP_597797 4.00E-44 Togaviridae Reference virus polyprotein precursor Sequences nsP1234 NCBI Protein Whataroa virus non-structural YP_008888546 1.00E-43 Togaviridae Reference polyprotein precursor Sequences nsP1234 NCBI Protein Western equine nonstructural protein NP_818936 2.00E-43 Togaviridae Reference encephalitis virus nsP4 Sequences NCBI Protein Venezuelan putative nonstructural NP_740699 6.00E-43 Togaviridae Reference equine protein nsP4 Sequences encephalitis virus NCBI Protein Southern elephant non-structural YP_008888545 2.00E-42 Togaviridae Reference seal virus polyprotein precursor Sequences nsP1234 NCBI Protein Eilat virus non-structural YP_008901141 3.00E-42 Togaviridae Reference polyprotein precursor Sequences nsP1234 NCBI Protein Eastern equine NS4 NP_740652 4.00E-42 Togaviridae Reference encephalitis virus Sequences NCBI Protein Aura virus Nonstructural protein NP_819013 3.00E-41 Togaviridae Reference nsP4 Sequences NCBI Protein Highlands J virus nsP4 YP_002802304 2.00E-40 Togaviridae Reference Sequences NCBI Protein Potato yellow vein RNA-dependent RNA YP_829128 4.00E-18 Closteroviridae Reference virus polymerase Sequences NCBI Protein Beihai charybdis RdRp YP_009333242 2.00E-15 unclassified Reference crab virus 1 Sequences NCBI Protein Hubei virga-like RdRp YP_009337693 3.00E-14 unclassified 4 Reference virus 15 Sequences NCBI Protein Olive latent virus 2 2a protein NP_620043 2.00E-11 Bromoviridae Reference Sequences NCBI Protein Grapevine RdRp gene product YP_004901687 2.00E-11 Closteroviridae Reference leafroll-associated Sequences virus 5 NCBI Protein Grapevine POL gene product YP_004940642 3.00E-11 Closteroviridae Reference leafroll-associated Sequences virus 1 NCBI Protein Blueberry virus A RNA dependent RNA YP_006638806 3.00E-11 Closteroviridae Reference polymerase Sequences NCBI Protein Parietaria mottle p2 protein YP_006447 8.00E-11 Bromoviridae Reference virus Sequences NCBI Protein Hubei virga-like RdRp YP_009337412 2.00E-10 unclassified Reference virus 2 Sequences NCBI Protein Adelphocoris ORF1 YP_009336476 4.00E-10 unclassified Reference suturalis virus Sequences NCBI Protein Grapevine RNA-dependent RNA YP_009241367 9.00E-10 Closteroviridae Reference leafroll-associated polymerase, partial Sequences virus 13 NCBI Protein Alfalfa mosaic 89.7 kd protein YP_053235 1.00E-09 Bromoviridae Reference virus Sequences NCBI Protein Hubei virga-like RdRp YP_009336553 1.00E-09 unclassified Reference virus 9 Sequences NCBI Protein Tobacco streak putative viral NP_620768 1.00E-09 Bromoviridae Reference virus polymerase Sequences NCBI Protein Ageratum latent RNA-dependent RNA YP_008470970 2.00E-09 Bromoviridae Reference virus polymerase Sequences NCBI Protein Grapevine polyprotein NP_813795 3.00E-09 Closteroviridae Reference leafroll-associated 5 Sequences virus 3 NCBI Protein Tulare apple putative polymerase NP_620754 6.00E-09 Bromoviridae Reference mosaic virus p2 Sequences NCBI Protein Citrus leaf rugose RNA-dependent RNA NP_613281 1.00E-08 Bromoviridae Reference virus polymerase Sequences NCBI Protein Blueberry shock replicase P2 YP_008519305 1.00E-08 Bromoviridae Reference virus Sequences NCBI Protein Grapevine RNA dependent RNA YP_002364303 2.00E-08 Closteroviridae Reference leafroll-associated polymerase, partial Sequences virus 10 NCBI Protein Prunus necrotic polymerase p2 NP_733824 2.00E-08 Bromoviridae Reference ringspot virus Sequences NCBI Protein Brome mosaic RNA-dependent RNA NP_041197 3.00E-08 Bromoviridae Reference virus polymerase Sequences NCBI Protein Culex negev-like RdRp YP_009388585 3.00E-08 unclassified Reference virus 1 Sequences NCBI Protein Blackberry p2 protein YP_002308570 5.00E-08 Bromoviridae Reference chlorotic ringspot Sequences virus NCBI Protein Humulus p2 protein YP_054423 6.00E-08 Bromoviridae Reference japonicus latent Sequences virus NCBI Protein Strawberry RdRp YP_941472 9.00E-08 Bromoviridae Reference necrotic shock Sequences virus NCBI Protein Privet leaf Replication-associated YP_009305430 2.00E-07 Idaeovirus Reference blotch-associated polyprotein Sequences virus NCBI Protein Asparagus virus 2 polymerase YP_002455929 2.00E-07 Bromoviridae Reference Sequences NCBI Protein Fragaria RNA-dependent RNA YP_164802 3.00E-07 Bromoviridae Reference chiloensis latent polymerase Sequences virus 6 NCBI Protein Black currant leaf nonstructural YP_009361854 8.00E-07 Idaeovirus Reference chlorosis polyprotein Sequences associated virus NCBI Protein Hubei virga-like hypothetical protein YP_009337659 8.00E-07 unclassified Reference virus 21 Sequences NCBI Protein Privet ringsport replication-associated YP_009165997 9.00E-07 Bromoviridae Reference virus polyprotein 2a Sequences NCBI Protein Elm mottle virus polymerase NP_619575 1.00E-06 Bromoviridae Reference Sequences NCBI Protein Wuhan RdRp YP_009342329 4.00E-06 unclassified Reference heteroptera virus Sequences 1 NCBI Protein Prune dwarf virus polymerase P2 YP_611151 4.00E-06 Bromoviridae Reference Sequences NCBI Protein Streptocarpus putative replicase YP_762617 1.00E-05 Virgaviridae Reference flower break virus Sequences 15 16 Table S3: Blastp hit list of predicted ORF2. Database virus protein accession e-value family non-redundant Venezuelan equine structural ADA84123 8.00E-20 Togaviridae protein encephalitis virus polyprotein sequences non-redundant Eastern equine structural ADB08675 2.00E-19 Togaviridae protein encephalitis virus polyprotein sequences non-redundant Madariaga virus structural AHL83773 2.00E-19 Togaviridae protein polyprotein sequences NCBI Protein Eastern equine E1 protein NP_740648 3.00E-18