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 Togaviridae Reference encephalitis virus Sequences NCBI Protein Venezuelan equine structural NP_040824 9.00E-18 Togaviridae Reference encephalitis virus polyprotein

7

Sequences precursor NCBI Protein Mayaro virus envelope NP_740694 2.00E-16 Togaviridae Reference glycoprotein E1 Sequences NCBI Protein Aura virus E1 protein NP_819019 4.00E-16 Togaviridae Reference Sequences NCBI Protein Chikungunya virus structural NP_690589 6.00E-16 Togaviridae Reference polyprotein Sequences NCBI Protein Whataroa virus unnamed YP_005351237 1.00E-14 Togaviridae Reference protein product Sequences NCBI Protein Tai Forest structural YP_009333616 2.00E-14 Togaviridae Reference alphavirus polyprotein Sequences NCBI Protein Sindbis virus e-1 structural NP_740677 2.00E-14 Togaviridae Reference protein Sequences NCBI Protein Fort Morgan virus E1 protein YP_003324599 8.00E-14 Togaviridae Reference Sequences NCBI Protein Getah virus C-P62-6K-E1 YP_164439 2.00E-13 Togaviridae Reference polyprotein Sequences NCBI Protein Bebaru virus unnamed YP_005351239 4.00E-13 Togaviridae Reference protein product Sequences NCBI Protein Eilat virus structural YP_006732328 1.00E-10 Togaviridae Reference protein Sequences 17

18 Table S4: GenBank/protein accession numbers for the phylogenetic analysis of the RdRp

19 sequences.

Name Abbrevation Family/Genus Interva Accession l (aa) Chikungunya virus strain CHIKV Togaviridae/ 2,153- AAN05101 S27-African Alphavirus 2,395

8

Getah virus from South Korea GETV Togaviridae/ 2,146- AAU85259 Alphavirus 2,388 Eastern equine encephalitis EEEV-I Togaviridae/ 2,176- ABL84686 virus strain FL93-939 Alphavirus 2,418 O'nyong-nyong virus strain ONNV Togaviridae/ 2,192- AAC97204 SG650 Alphavirus 2,434 Ross River virus strain 9057 RRV Togaviridae/ 2,160- ACV66999 Alphavirus 2,402 Semliki forest virus 42S SFV Togaviridae/ 2,107- CAA27741 Alphavirus 2,349 Sindbis virus isolate SW6562 SINV Togaviridae/ 2,166- AAM10628 Alphavirus 2,408 Sleeping disease virus SDV Togaviridae/ 2,275- CAC87660 Alphavirus 2,517 Venezuelan equine VEEV-IAB Togaviridae/ 2,175- AAC24033 encephalitis virus strain Alphavirus 2,417 71-180 Western equine WEEV Togaviridae/ 2,149- AAF28339 encephalomyelitis virus strain Alphavirus 2,390 71V-1658 Tobacco streak virus TSV Bromoviridae/ 385- AAB48409 Ilarvirus 625 Brome mosaic virus BMV Bromoviridae/ 387- CAA25834 Bromovirus 619 Cowpea chlorotic mottle virus CCMV Bromoviridae/ 398- NP_613275.1 Bromovirus 630 Peanut stunt virus PSV Bromoviridae/ 426- BAA01901 Cucumovirus 658 Cucumber mosaic virus CMV Bromoviridae/ 439- BAA00263 Cucumovirus 671 Broad bean mottle virus BBMV Bromoviridae/ 398- AAA42741 Bromovirus 630 Tomato aspermy virus TAV Bromoviridae/ 443- BAA01514 Cucumovirus 675 Tobacco mosaic virus TMV Virgaviridae/ 1,303- NP_597746 Tobamovirus 1,541 Barley stripe mosaic virus BSMV Virgaviridae/ 449- AAA66600 Hordeivirus 685 Soil-borne wheat mosaic virus SBWMV Virgaviridae/ 1,505- NP_049335 Furovirus 1,742 Pea early-browning virus PEBV Virgaviridae / 1,433- CAB37343 Tobravirus 1,670 Tobacco rattle virus TRV Virgaviridae/ 1,373- BAA00110 - 1,610 Potato virus X PVX Alphaflexiviridae/ 1,161- P09395 Potexvirus 1,390 Strawberry mild yellow edge SMYEAV Alphaflexiviridae/ 1,030- BAA02082 virus Potexvirus 1,258 9

Shallot virus X ShVX Alphaflexiviridae/ 1,339- AAA47787 Allexivirus 1,562 Turnip yellow mosaic TYMV Tymoviridae/ 1,498- CAA30322 Tymovirus 1,720 Eggplant mosaic virus EPMV Tymoviridae/ 1,494- AAA43039 Tymovirus 1,715 Ononis yellow mosaic virus OYMV Tymoviridae/ 1,424- AAA46796 Tymovirus 1,645 Kennedya yellow mosaic virus KYMV Tymoviridae/ 1,528- BAA00532 Tymovirus 1,749 Garlic virus A GarV-A-JA Alphaflexiviridae/ 1,257- NP_569126 Allexivirus 1,480 Oryza sativa endornavirus OsEV Endornaviridae/ 4,240- YP_438200 Endornavirus 4,477 Hepatitis E virus HEV-1 Hepeviridae/ 1,382- AAA45734 Hepevirus 1,609 Hepatitis E virus Ct1 HEV-4 Hepeviridae/ 1,396- Q9IVZ9 Hepevirus 1,623 Avian hepatitis E virus aHEV-1 Hepeviridae/ 1,222- CAQ16027 - 1,450 Vicia faba endornavirus VfEV-447 Endornaviridae/ 5,396- YP_438201 Endornavirus 5,632 Phytophthora endornavirus 1 PEV1-OR Endornaviridae/ 4,280- YP_241110 Endornavirus 4,517 Beet yellows virus BYV Closteroviridae/ 2,720- AAC25115 Closterovirus 2,956 Mint virus 1 MV1 Closteroviridae/ 110- YP_224091 Closterovirus 347 Plum bark necrosis stem PBNSTaV Closteroviridae/ 190- YP_001552324 pitting-associated virus Ampelovirus 427 Little cherry virus 2 LChV-2 Closteroviridae/ 1,831- NP_891562 Ampelovirus 2,068 20 21

22 Table S5: GenBank/protein accession numbers for the phylogenetic analysis of the Helicase

23 sequences.

Name Abbrevation Family/Genus Interva Accession l (aa) Chikungunya virus strain CHIKV Togaviridae/ 720- AAN05101 S27-African Alphavirus 959 Getah virus from South Korea GETV Togaviridae/ 719- AAU85259 Alphavirus 958 Eastern equine encephalitis EEEV-I Togaviridae/ 718- ABL84686 virus strain FL93-939 Alphavirus 956

10

O'nyong-nyong virus strain ONNV Togaviridae/ 720- AAC97204 SG650 Alphavirus 959 Ross River virus strain 9057 RRV Togaviridae/ 719- ACV66999 Alphavirus 958 Semliki forest virus 42S SFV Togaviridae/ 722- CAA27741 Alphavirus 961 Sindbis virus SINV Togaviridae/ 725- NP_062889 Alphavirus 967 Sleeping disease virus SDV Togaviridae/ 749- CAC87660 Alphavirus 988 Venezuelan equine VEEV-IAB Togaviridae/ 720- AAC24033 encephalitis virus strain Alphavirus 946 71-180 Western equine WEEV Togaviridae/ 718- AAF28339 encephalomyelitis virus strain Alphavirus 956 71V-1658 Brome mosaic virus BMV Bromoviridae/ 684- NP_041196 Bromovirus 946 Cowpea chlorotic mottle virus CCMV Bromoviridae/ 681- NP_613278 Bromovirus 943 Peanut stunt virus PSV Bromoviridae/ 721- P28726 Cucumovirus 984 Cucumber mosaic virus CMV Bromoviridae/ 713- NP_049323 Cucumovirus 976 Broad bean mottle virus BBMV Bromoviridae/ 689- NP_659000 Bromovirus 951 Tomato aspermy virus TAV Bromoviridae/ 713- NP_620760 Cucumovirus 976 Tobacco mosaic virus TMV Virgaviridae/ 832- NP_597746 Tobamovirus 1,084 Barley stripe mosaic virus BSMV Virgaviridae/ 837- NP_604474 Hordeivirus 1,109 Soil-borne wheat mosaic virus SBWMV Virgaviridae/ 1,026- NP_049335 Furovirus 1,288 Pea early-browning virus PEBV Virgaviridae / 962- CAB37343 Tobravirus 1,214 Tobacco rattle virus TRV Virgaviridae/ 903- BAA00110 - 1,155 Potato virus X PVX Alphaflexiviridae/ 734- P09395 Potexvirus 963 Strawberry mild yellow edge SMYEAV Alphaflexiviridae/ 604- BAA02082 virus Potexvirus 833 Shallot virus X ShVX Alphaflexiviridae/ 914- AAA47787 Allexivirus 1,142 Turnip yellow mosaic TYMV Tymoviridae/ 975- CAA30322 Tymovirus 1,204 Eggplant mosaic virus EPMV Tymoviridae/ 964- AAA43039 Tymovirus 1,192 11

Ononis yellow mosaic virus OYMV Tymoviridae/ 989- AAA46796 Tymovirus 1,127 Kennedya yellow mosaic virus KYMV Tymoviridae/ 1,001- BAA00532 Tymovirus 1,234 Garlic virus A GarV-A-JA Alphaflexiviridae/ 831- NP_569126 Allexivirus 1,059 Hepatitis E virus HEV-1 Hepeviridae/ 974- AAA45734 Hepevirus 1,184 Hepatitis E virus Ct1 HEV-4 Hepeviridae/ 988- Q9IVZ9 Hepevirus 1,198 Avian hepatitis E virus aHEV-1 Hepeviridae/ 817- CAQ16027 - 1,026 Beet yellows virus BYV Closteroviridae/ 2,248- AAC25115 Closterovirus 2,516 Mint virus 1 MV1 Closteroviridae/ 2,135- YP_224090 Closterovirus 2,397 Plum bark necrosis stem PBNSTaV Closteroviridae/ 2,046- YP_001552323 pitting-associated virus Ampelovirus 2,309 Little cherry virus 2 LChV-2 Closteroviridae/ 1,344- NP_891562 Ampelovirus 1,606 24

12