sign in sign up
<<
Home , Benyvirus, Furovirus, Ilarvirus, Pecluvirus, Tobravirus

Template for Taxonomic Proposal to the ICTV Executive Committee To create a new Family

† Code 2007.036P To create a new family* in an existing Order° Unassigned

† Code 2007.037P To name the new family*

† Code 2007.038P To designate the following genera as part of the new family*: † Assigned by ICTV officers ° Leave blank is not appropriate * repeat these lines and the corresponding arguments for each genus created in the family Author(s) with email address(es) of the Taxonomic Proposal Mike Adams ([email protected]) Jan Kreuze ([email protected])

Old Taxonomic Order Order Unassigned Family Unassigned Genus Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, Tobravirus New Taxonomic Order Order Unassigned Family Virgaviridae Genus Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, Tobravirus

ICTV-EC comments and response of the SG Argumentation to create a new family:

The new family groups together 6 currently unassigned genera of ssRNA plant that are characterised by: 1. Single-stranded RNA + sense genomes with a 3’- t-RNA like structure and no polyA tail 2. Rod-shaped virions 20-25nm in diameter with a central “canal” 3. Alpha-like replication proteins that form a distinct phylogenetic “family” (Koonin & Dolja, 1993) 4. Coat proteins of 19-24kDa 5. Movement proteins that are either a single protein of the ‘30K’ superfamily (Melcher, 2000) or from a distinct subset of TGBs (Morozov & Solvyev, 2003)

This includes all the rod-shaped plant viruses except those of the genus that are much more distantly related in phylogenetic analyses. The genera themselves are justified largely on the basis of genome organization (Fig. 1) and phylogenetic analysis and their major properties are summarized in Table 1.

Table 1. Major properties of the genera proposed for inclusion in the new family Virgaviridae (See also Fig. 1)

Genus RdRPa MPb CPc 3’ structured Transmission Furovirus 2 RT ‘30K’ 19K+RT t-RNAVal “fungus” Hordeivirus 3 Separate TGB 22K t-RNATyr seed Pecluvirus 2 RT TGB 23K t-RNAVal “fungus” + seed Pomovirus 3 RT TGB 20K+RT t-RNAVal “fungus” Tobamovirus 1 RT ‘30K’ 17-18K t-RNAHis mechanical Tobravirus 2 RT ‘30K’ 22-24K t-RNA- nematode

a relation of RdRp to the replication protein (Methyltransferase, Helicase); RT, in a readthrough domain at the C-terminus b MP, movement protein either of the ‘30K’ superfamily (Melcher, 2000) or a Triple gene block (TGB; Morozov & Solovyev, 2003) c CP, coat protein size (with indication of RT, a readthrough domain at the C-terminus if present) d t-RNAVal/Tyr/His/-, t-RNA like structure accepting Valine, Tyrosine, Histidine or not aminoacylated respectively

The only genus with rod-shaped virions excluded from this list is Benyvirus because this is much more distantly related in phylogenetic analyses of the polymerase (see below) and because (unlike the others) its members have a polyadenylated genome, and the polymerase is processed by autocatalytic protease activity.

1. The replication protein More than 10 years ago, Koonin & Dolja (1993) included all these viruses within RdRp Supergroup 3, which they sub-divided into 3 lineages that they suggested might correspond to Orders: Tymo (including tymoviruses and the genera that we now have in the family Flexiviridae), Rubi (including benyviruses, and others) and Tobamo (including the viruses in the 6 genera considered here together with , and ). Phylogenetic analysis of the RdRp domain, of the whole replication protein or of the fused Met-Hel-RdRp domains continues to support this grouping (see Fig. 2).

The replication proteins constitute the majority of the genomes of these viruses and provide the best phylogenetic trees but there are also indications of relatedness amongst the other genes (see below). 2. The movement proteins (a) The ‘30K’ proteins of Furovirus, Tobamovirus and Tobravirus are related but do not form a coherent subgroup of MPs as those of Furovirus are more closely related to those of and Bromoviridae than to the other rod-shaped genera (Melcher, 2000) (Fig. 3).

(b) The Triple gene block (TGB) proteins of the genera Hordeivirus, Pecluvirus and Pomovirus are clearly related, while those from the genus Benyvirus are more distantly related. A tree for TGBp1 sequences is provided in Fig. 4. The only other viruses with a TGB module are from the filamentous viruses in the family Flexiviridae. The TGBs of the rod shaped viruses differ from these in having a larger TGBp1 and TGBp3 (the latter having two, rather than one, transmembrane domains) and form a distinct group in phylogenetic anlayses. For more details supporting this classification of the TGB proteins, see Morozov & Solovyev (2003).

3. The coat proteins The small size of the coat protein and its inherent variability make it less suitable for phylogenetic analysis. Nevertheless, significant groupings of genera occur (Furo- with Pomo-; Peclu- with Hordei- and Tobra- a bit more distant) which correspond with those found within the RdRp (Fig. 5).

4. The small cysteine-rich proteins There are close relationships between the small cysteine-rich proteins of Furovirus, Hordeivirus, Pecluvirus and Tobravirus (Fig. 6) although those of Pomovirus do not align well with them.

Origin of the proposed family name

From virga (Latin = rod) from the morphology of the virions.

References Koonin, E.V. & Dolja, V.V. (1993). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol., 28, 375-430. Melcher, U. (2000). The '30K' superfamily of viral movement proteins. J Gen Virol., 81, 257-266. Morozov, S.Y. & Solovyev, A.G. (2003). Triple gene block: modular design of a multifunctional machine for plant movement. J Gen Virol., 84, 1351-1366. Annex:

Pomovirus M H R tVal tVal tVal

Furovirus M H R tVal tVal

M H Tyr Tyr Hordeivirus t R t tTyr

Pecluvirus M H R tVal tVal

Tobamovirus M H R tHis

Tobravirus M H R

t - t -

7 Kb

Figure 1. Diagram showing the genome organisation of the 6 genera proposed for inclusion in the family Virgaviridae. Replication proteins are shown in blue with the methyltransferase (M), helicase (H) and RdRp (R) domains. Coat proteins are in red, ‘30K’-type movement proteins in green, triple gene block movement protein modules in yellow and cysteine-rich proteins in grey. Other ORFs are shown in white and positions of “leaky” stop codons by triangles (►). tVal/Tyr/His/-: t-RNA like structure accepting Valine, Tyrosine, Histidine or not aminoacylated respectively. Brackets indicate ORFs that are missing from some strains. WMoV YMoV TVCV ORSV SFBV 100 TMGMV ObPV PMMoV ToMV ReMV Tobamovirus 100 TMV HLSV CuMoV CGMMV 100 CFMMV 99 KGMMV Proposed Virgaviridae ZGMMV PEBV 100 PepRSV Tobravirus TRV 100 IPCV 83 PCV Pecluvirus 100 BSMV Hordeivirus BVQ 62 PMTV Pomovirus 100 47 BSBV BBNV OGSV 100 SrCSV Furovirus CWMV 57 100 SBWMV SBCMV

100 Idaeovirus 97 Bromoviridae 88 Closteroviridae 81 Citrus leprosis virus 100 100 55 BotVX 98 Potex & 67 51 SsDRV 84 BotVF 53 100 97 Proposed 100 99 100 40 52 20 BanMMV 100 CGRMV 92 CNRMV 85 Carla & 59 Benyvirus 100

0.5

Figure 2. Phylogenetic (Neighbor-joining) tree of the amino acid sequences of the fused Met-Hel-RdRp domains of the members of the 6 genera proposed for inclusion in the family Virgaviridae (pale blue) together with other related viruses. Distantly related genera and families which formed well-supported monophyletic clades were collapsed into a triangle, the length of which corresponds to the variation found within the clade. Numbers on branches indicate percentage of bootstrap support out of 1000 bootstrap replications. Scales indicate JTT amino acid distances. Tobamovirus

PZSV 85 85 OLV-2

CMV

61 Tobravirus 85 BMV

Furovirus 64 TSV 77 AMV Alfamovirus 0.1 Dianthovirus

Figure 3. Phylogenetic (Neighbor-joining) tree of the amino acid sequences of the ‘30K’ movement proteins of members of the genera (circled) proposed for inclusion in the family Virgaviridae together with other related viruses.

Pecluvirus

P P C D BBNV C V - -H V - V V L - M C C - N P P V i I I C PCV-B IP PCV-N PCV-87 BSMV 79 Hordeivirus Pomovirus

100 PSLV BSBV

100 79 BVQ

LRSV PMTV Figure 4. Phylogenetic (Neighbor-joining) tree of the amino acid sequences of the TGBp1 proteins of members of the genera proposed for inclusion in the family Virgaviridae together with other related 100 viruses.

BNYVV 100

BSBMV 0.1 Benyvirus

NVMV 1 = YoMV Tobamovirus 2 = WMoV 3 = TVCV 4 = RMV 5 = PaMMV

V 6 = ObPV

V M 7 = ORSV ZGMMV V M M V S r P G L F 8 = TMV F 1 2 K H 3 CFMMV L 4 9 = ToMV H 6 7 10 = TMGMV PepRSV 100 5 8 9 11 = TLV SHMV 10 11 12 = PMMoV CGMMV 12 NVMV PEBV 94 Tobravirus 99 Pomovirus 99 BSBV TRV 96

64 BVQ 84 PMTV

98

IPCV-D 69 BBNV 85 IPCV-H 99 PCV-87 IPCV-L 91 Pecluvirus SrCSV 99 CWMV O 94 SB GS S W V- BSMV SBWMV-J BC M U M V K 100 V BNYVV 0.1 PSLV BSBMV LRSV Hordeivirus Benyvirus Furovirus

Figure 5. Phylogenetic (Neighbor-joining) tree of the amino acid sequences of the coat proteins of members of the genera proposed for inclusion in the family Virgaviridae together with other related viruses.

Furovirus CWMV Hordeivirus OGSV SBCMV 74 LRSV SBWMV 83

SrCSV PSLV

BSMV

96 IPCV PCV Pecluvirus PepRSV 0.1 68 86 PEBV

TRV Tobravirus

Figure 6. Phylogenetic (Neighbor-joining) tree of the amino acid sequences of the cysteine-rich proteins of members of four genera proposed for inclusion in the family Virgaviridae.