The potyviruses of Australia – Electronic Supplementary Material. Notes on the potyviruses found in Australia, and the relationships of their ccp sequences; data collected in 2005-7

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The potyviruses of Australia – Electronic Supplementary Material.
Notes on the potyviruses found in Australia, and the relationships of their cCP sequences; data collected in 2005-7.
Apium virus Y (ApVY) is widespread in Australia [24]. It has been isolated from Conium maculatum (poison hemlock), Apium prostratum (sea celery) and Petroselinum crispum (parsley), all showing mosaic symptoms. It has been also found in New Zealand and is common in Germany in parsley and dill (Anethum graveolens) (H. Josef Vetten, personal communication). In Australia isolates have been transmitted by sap inoculation to several apiaceous species including celery, chervil, coriander, dill and parsley causing necrotic and chlorotic mosaics, it gave chlorotic local lesions in Chenopodium quinoa, but did not infect basil, Chinese cabbage, eggplant, French bean (Phaseolus vulgaris), Gomphrena globosa, Nicotiana glutinosa, okra, parsnip, pea (Pisum sativum), petunia (Petunia hybrida) or tobacco (Nicotiana tabacum). No infected plants were obtained among seedlings from several thousand seeds from ApVY-infected Conium maculatum. Of the three species found to be naturally infected with ApVY only Apium prostratum is an indigenous Australian species (, parsley is a widely cultivated herb that is a native of southern Europe and used since at least Roman times [28], and Conium maculatum is a weed species distributed widely around the world but originally from Europe.

The cCP regions of three distinct isolates of ApVY have been determined (AF207594, AF203529 and AY049716). The original isolate came from a sample of C. maculatum collected by B.D. Harrison near Cooma, New South Wales, and the others from parsley from Western Australia and from Queensland. The average divergence of the three cCPs is 0.0253 ud/s. The most closely related cCP sequences to the ApVY sequences are those of carrot virus Y and celery mosaic virus with mean divergences of 0.248 ud/s and 0.232 ud/s respectively, and more distantly related are all cCPs of other potyvirus species. The partial cCP sequence (EU127499) of a New Zealand isolate has been reported, it is 97% identical to the Australian sequences.

Bean common mosaic virus (BCMV) is found in crops of the common bean (Phaseolus vulgaris) worldwide and of many other legumes [5, 23], and is transmitted to a large proportion of the seed of infected plants. It has been reported from many parts of Australia for many years [6] but was only recently recorded in Western Australia [29]. That report included the cCP sequence of an isolate (AY850005), which differed by only 0.03 ud/s from those of the Type and NL1 isolates of the virus, but up to 0.14 ud/s from the homologous region of several other isolates of the species including those called peanut stripe virus. BCMV was originally one of several potyviruses isolated from various forage and pulse legumes and given different names. However many of these have been shown to be so closely related that they are now grouped as strains of BCMV. They were/are called blackeye cowpea mosaic virus (BlCMV), azuki bean mosaic, dendrobium mosaic virus (DMV) and peanut stripe virus (PStV) [31] and all, except DMV, have been shown to be seed-borne. BCMV has a very large experimental host range, especially among pulses and other legumes.
Bean yellow mosaic virus (BYMV) is a well characterized virus found worldwide [5]. It has most often been isolated from legumes and various monocotyledonous bulb and orchid species, notably cultivated Gladiolus spp., natives of southern Africa. The most fully characterized Australian BYMV isolates were isolated from peas in Victoria [22, 34]. In West Australia BYMV has been isolated from several legume species [18, 21, 42, 43], including Kennedya prostrata, a native species, and it has also been found in orchid collections in the eastern states [11].

BYMV is genetically variable with divergences up to 0.159 ud/s. Fig 6 shows the relationships of a representative sample of the cCP sequences of 52 BYMV isolates and 19 isolates of the closely related clover yellow vein virus, including several from Australia (AF042272; AF185960/62; AF192781-3, AF434661; AY376314, AY397612, S77515, U47033, U78191 and X81124, DQ901431-5, AJ844916, AB041972 and X53684).

There are several distinct lineages of BYMV cCPs and Australian isolates are found in most of them (Fig 6). There is also no correlation between the phylogenetic relationships of different isolates and their provenance or the host from which they were isolated; the lineages all contain isolates from both mono- and dicotyledonous hosts and one cluster, for example, contains 12 Australian isolates from forage legumes, Lupinus angustifolius and Melilotus indicus, the native legume, Kennedya prostrate [42], the orchids Diurus maculata and Pterostylis curta with the remainder coming from Gladiolus spp. from North America, Japan, India and Europe! The simplest interpretation of this phylogenetic tree is that the world population of BYMV has several lineages, and isolates from at least four of them have been imported into Australia. International trade, especially in gladioli and other bulbs as ornamentals, is probably responsible for the worldwide distribution of BYMV, but it may also have been transported in forage legume seed
Carrot virus Y (CarYV) is widespread and damaging in Australia where it is found in feral and crop carrots in all the southern States [19, 24]. Like ApVY it is readily transmitted by sap inoculation to a range of apiaceous plants, and like the related viruses, ApVY and celery mosaic virus, has a limited host range. The carrot, Daucus carota, is an ancient crop of the Mediterranean region, and only grew wild throughout Europe, Asia and Africa [16, 28], but has become feral wherever the crop is grown, including Australia. The cCP sequences of CarVY from carrots from Victoria, Western Australia and New South Wales (AF203537, AF203538, AF 203539) differ by only 0.007 ud/s. The cCP sequences most closely related to those of CarVY are from celery mosaic virus (mean divergence 0.191 ud/s) and ApVY (mean divergence 0.248 ud/s). It seems most likely that CarVY is a recent migrant to Australia, and that its overseas parent population has not yet been identified.
Celery mosaic virus (CeMV) is a well studied virus that has been found in many parts of the world [5]. In Australia CeMV is common in celery crops, but very rarely infects carrots in adjacent crops, although it readily infects carrots experimentally [24]. Celery (Apium graveolens) is a herb and vegetable crop of temperate regions, and grows wild as a marsh plant throughout temperate Europe and Asia [16, 28]. Australian CeMV isolates have the same biological properties as European and North American isolates, but form a sister lineage to those reported from elsewhere in the world [24]. The mean divergence of the cCP sequences from four Australian isolates (AF203532-5) is only 0.002 ud/s, but they differ by 0.020 ud/s from two European cCP sequences, which themselves differ by only 0.002 ud/s. This pattern of relationships suggests that the Australian CeMV population has come from a single incursion from overseas. The closest cCP sequences to those of CeMV are of ApVY (mean interspecies divergence 0.232 ud/s) and CarVY (mean divergence 0.191 ud/s).
Candidatus Ceratobium mosaic virus (CerMV) is a Candidatus potyvirus found in several orchids in glasshouse collections. It has only been reported from Australia, and is probably endemic. Infected plants show chlorotic and necrotic mosaic and mottling [11, 20], CerMV has not been transmitted experimentally. It was found most often in orchids of the Ceratobium group of Dendrobium species, but also in orchids of 19 other genera [11]. Five CerMV cCPs sequences have been reported (AF022442- AF022446) and found to have divergences varying from 0.025 ud/s to 0.103 ud/s (mean 0.061 ud/s +/- 0.028 ud/s). A search of the public databases using the CerMV sequences found no sequences to be more closely related to CerMV than those of peanut stripe virus (0.232 ud/s) and zucchini yellow mosaic virus (0.257 ud/s) (Fig 7).
Candidatus Clitoria virus Y (CliVY) is another member of the BCMV lineage, known only from a gene sequence (AF228515) from the mottled leaves of a single plant of Clitoria ternatea from a building site in central Townsville, Qld. The cCP sequence recovered from this specimen is closest to those of different isolates of passionfruit woodiness virus with divergences ranging from 0.028 ud/s to 0.187 ud/s (Fig 7).
Clover yellow vein virus (CYVV), like its close relative BYMV, has also been reported from many parts of the world and is widespread in Australia where it has been isolated from lupins in the Rutherglen area of Victoria [40], from the apiaceous species Ammi majus (bishop’s weed) and Hydrocotyle spp. also from Victoria [24] and from a Cuban Royal Palm (Roystonia regia; Arecaceae) growing in Queensland (AF203536, AF185959, S77521, AY169801). Many CYVV cCP sequences have been reported, most from Japan. They fall into two distinct lineages (Fig 6) that have mean interlineage divergences of around 0.158 ud/s; one of the lineages has been found only in Japan. Australian CYVV cCPs do not form a distinct group. All CYVV cCPs differ from those of BYMV by around 0.27 ud/s.

Candidatus Dianella chlorotic mottle virus (DiCMV), which is only known from the 5′ terminal half of its cCP gene sequence (DQ075247). It was obtained from mottled leaves of a plant of Dianella spp. (Flax Lily; Phormiaceae) collected in Victoria (Table 1), and is closest to the homologous region of the cCP of fritillary virus Y, a member of the BCMV lineage from China.

Candidatus Diuris virus Y (DiVY) is another Candidatus potyvirus found in the mottled leaves of Diurus orientis, an Australian endemic herbaceous terrestrial orchid. It was found in plants from several localities in western Victoria [11]. It is probably the first virus to be reported from an orchid in the wild, as all others have been obtained from plants in orchid collections. A cCP sequence from one isolate (AF203527 AF203527) was closest (0.298 ud/s) to that of zucchini yellow mosaic virus indicating that it is a distinct species of the BCMV lineage (Fig 7).
Euphorbia ringspot virus (ERV), which was obtained from a Euphorbia spp. plant imported from Thailand and intercepted in quarantine in Queensland. Its partial cCP sequence (AY517544) is closely similar (divergence 0.02 ud/s) to that of an isolate from a specimen of Euphorbia milli var. splendens (Crown of Thorns) of unknown origin in the USA [13]. These cCP sequences differ by 0.15-0.18 ud/s from those of several viruses common in ornamental bulb species including tulip mosaic, tulip breaking and iris severe mosaic viruses. There is no evidence that this virus is established in Australia.
Candidatus Eustrephus virus Y (EustVY) is known only from gene sequences obtained from the mottled and striped leaves of Eustrephus latifolius, a shrubby monocotyledonous climber common in the understorey of the coastal woodlands of southern New South Wales. E. latifolius plants show clear necrotic and chlorotic striping. The symptoms are especially obvious in younger leaves, and in the cooler months. Attempts to transmit from these by sap inoculation to a range of standard indicator plants failed. The cCP sequence of only one specimen has been determined (DQ098904). This sequence is closest to that of Sarcochilus virus Y (Fig 7) (divergence 0.175 ud/s) and next closest to those of soybean mosaic virus (divergence 0.27 ud/s) showing that it is another BCMV lineage virus.
Candidatus Glycine virus Y (GVY) is known only from a partial NIb sequence (DQ098902) obtained from leaves of Glycine clandestina, a small herbaceous climbing legume, showing clear mosaic symptoms and growing on Nuggan Point, Termeil, New South Wales. Mosaics and mottling are common in this species which is widespread in New South Wales. The partial sequence is most similar to that of ornithogalum mosaic virus.
Hardenbergia mosaic virus (HarMV) is a potyvirus from Hardenbergia comptoniana, a native plant found in the south west of Western Australia (WA) [42]. H. comptoniana showing the mosaic symptoms of HarMV are widespread in the south west of WA and were found in plants at all 12 sites sampled. The cCP sequences of 28 isolates of HarMV from WA have been reported (DQ898188-214, EF375606-8) [42]. They vary and have divergences of up to 0.159 ud/s. HarMV is probably being spread from WA by the horticultural trade; the cCP sequences of two isolates from H. comptoniana growing in a Canberra garden are closest (divergence 0.008 ud/s) to those of isolates from central Perth in WA. HarMV has also been isolated from a plant of the related Hardenbergia violacea, a native of south eastern Australia, found in a plant nursery in Perth and showing mosaic symptoms. However surveys of wild H. violacea in eastern Australia over several decades failed to find plants with similar symptoms. HarMV cCPs are most closely related to those of Australian passionfruit woodiness viruses and others of the BCMV lineage (Fig 7); the closest is that of an isolate from Queensland (AJ430527, divergence 0.21 ud/s).
Candidatus Hibbertia virus Y (HibVY) is another Candidatus potyvirus. It was found in Hibbertia scandens, a shrubby scrambler with broad glossy leaves and showy yellow flowers common in the coastal woodlands of New South Wales. Repeated attempts to transmit the virus by sap inoculation to a standard range of indicator plants, and to H. scandens seedlings, failed. Infected plants have mottled leaves, and are common throughout the range of the host plant. The single cCP gene sequence (AF228516) was obtained from a specimen collected near Pretty Beach, Kioloa, New South Wales, and is closest to that of siratro 1 virus Y (divergence 0.182 ud/s) and other cCPs of the BCMV lineage (Fig 7).
Johnson grass mosaic virus (JGMV) is one of a complex of four distinct potyviruses of tropical grasses (Fig 5) that was not unequivocally resolved into its component species until their protein and gene sequences were determined [10, 30]. Only two of them, JGMV and sugarcane mosaic virus (SCMV), have been found in Australia. JGMV was first isolated from Johnson grass (Sorghum halepense) and maize in Queensland [34, 35], and is common in those hosts throughout the eastern half of Australia, especially east central and south east Queensland, and north east New South Wales. It was also isolated from 13 panicoid C4 grasses, but was not found in the chloridoids Eleusine and Eragrostis nor the pooid C3 Avena sativa, which are all susceptible in host range tests. Two of the natural panicoid hosts, Papalum orbiculare and Sorghum stipoideum, are native to northern and/or northeastern Australia. JGMV has also been isolated in North America and there are sequences of two cCPs from there. The Australian JGMV sequences (AF032404; AY387806-28; X05040, Z26920) [17] form a single cluster (mean divergence 0.042 ud/s, maximum 0.029 ud/s), and the two USA sequences form a sister lineage with a mean inter-lineage divergence of 0.075 ud/s (Fig 5). Although initially confused with SCMV and others of the SCMV lineage, JGMV is not a member of that lineage but is a separate potyvirus species.
Candidatus Kennedya virus Y (KVY) is found in plants of the leguminous scrambler Kennedya rubicunda, which is common in the temperate frost-free coastal regions of central and southern New South Wales, especially in recently disturbed areas, such as coastal sand dunes and roadsides. Many of the plants of this species show chlorotic and necrotic mosaic and mottling. KVY was found in those showing a mild marbling mosaic, whereas those with more severe symptoms are usually infected with kenndya yellow mosaic tymovirus [7, 32]. The sequence of part of the NIb gene of KVY (DQ098903) came from a specimen collected from a penguin colony on Bowen Island, New South Wales. Its sequence is most similar to that of the cCP of HibVY (divergence 0.10 ud/s) (Fig 7) indicating that it is also a member of the BCMV lineage .
Ornithogalum mosaic virus (OrMV) was obtained from a cultivated Iris plant showing chlorotic mosaic symptoms and growing in a spring flower show in Canberra. OrMV is widespread in bulb and other monocotyledonous species in all the major regions of the world, and has probably been spread worldwide in horticultural species especially bulbs. The cCP sequence of the Canberra isolate (AF203528) was closely similar (divergence 0.005 ud/s) to that of an isolate from Iris tingitana (AY994107) found in New Zealand, to another from Vanilla fragrans (AY845013; divergence 0.006 ud/s) found in Shimoga, India, and a third from Narcissus spp. (AJ493580; divergence 0.016 ud/s) found in Hangzhou, China. OrMV is a distinct but diverse species, and has inter-isolate divergences of up to 0.19 ud/s.

We also isolated a Candidatus virus, which we called pterostylis virus Y [11] (see below), and which had divergences of around 0.13 ud/s from the cCPs of some isolates of OrMV from Japan (AB079647/8/9). We are uncertain whether PtVY should be considered a strain of OrMV or a distinct species of an OrMV lineage.

Papaya ringspot virus (PRSV) [15] was first found in a papaya crop near Brisbane in 1990 [3]. When PRSV was first described it was shown to also infect a wide range of cucurbits, and could only be distinguished from another potyvirus of cucurbits, known as watermelon mosaic virus 1 [5, 41], by its ability to infect papaya. These two viruses are now known as the papaya and watermelon strains of PRSV, namely PRSV-P and PSRV-W.

The sequences of the cCP genes of over 200 isolates from around the world of PRSV, both -P and -W, have been reported. The Australian cCP sequences (U14736-40; U14744) form a monophyletic cluster (mean divergence 0.014 ud/s) within an American lineage of the virus; they are closest to isolates found in central America (divergences 0.026 ud/s); the nearest is an isolate from Yucatan, Mexico (AF319499) with others, slightly more distant, from Cuba, Puerto Rico and Mexico. The world population of PRSV has a basal divergence of 0.114 ud/s.

Candidatus Passiflora foetida virus Y (PfoVY) was found in a plant of Passiflora foetida growing at Ellis Beach, near Cairns, Queensland. Its cCP sequence (DQ112219) shows that it is a distinct member of the BCMV lineage closest to zucchini yellow mosaic virus (divergence 0.267 ud/s) (Fig 7). P. foetida is a common weed of the tropics originally from central and South America. Parry and colleagues [27] described Passiflora virus Y (PasVY) as a potyvirus of P. foetida from Papua, two Torres Strait islands and the Cape York Peninsula of Queensland. The three partial cCP sequences they obtained were 96-97% identical and came from the Papuan and island samples, however the recorded sequence (AY461661) was only 88% identical to that of PfoVY from Queensland. Thus it is likely that there are at least two BCMV lineage viruses of P. foetida, one in Papua and the islands, and the other in mainland Australia.
Passionfruit Woodiness is a disease of Passiflora spp. caused by various viruses of the BCMV lineage (Fig 7). It has been reported from cultivated passion fruit (Passiflora edulis) in New South Wales (NSW) [33], Queensland (Qld) [8, 27] and Western Australia (WA) [42]. The cCP sequences of eight Australian isolates have been reported (U67149-51; AJ430527; DQ898215-18). Four from WA and one from Queensland have a mean divergence of 0.041 ud/s, and three from NSW have a mean divergence of 0.037 ud/s, but these two groups of sequences are distinct and differ from one another by a mean of 0.177 ud/s (Fig 7). Both groups are most closely related to three Candidatus potyviruses found in eastern Australia, HibVY, S1VY and S2VY, and differ from these with mean divergences of 0.17-0.19 ud/s. Therefore it is uncertain whether the WA/Queensland group are members of a widespread northern Australian lineage, or whether the present distribution reflects recent plant trade between WA and Queensland.

Similar diseases and viruses of Passiflora spp. have also been reported from Brazil [12, 25], Japan [14], South Africa [4] and the USA [2]. These viruses are variously called passionfruit woodiness virus (PWV), East Asian passiflora virus, South African passiflora virus and Florida passionflower potyvirus, but those found in Brazil have been identified as isolates of cowpea aphid-borne mosaic virus (Fig 7). All these viruses are members of the BCMV lineage, and the simplest conclusion from their phylogenies is that passionflowers and P. edulis, which was originally domesticated in southern Brazil but has been distributed from there over the past two centuries and grown throughout the world [16, 28], are, like P. foetida, particularly susceptible to viruses of the BCMV lineage .

Pea seed-borne mosaic virus (PSbMV) is a distinct potyvirus species has been found in all the major regions of the world and, as its name indicates, is readily seed-borne. The sequences of the cCP genes of isolates, including one from Australia (AF127767) [1], have been determined. They form a single diverse population with divergences ranging up to 0.083 ud/s with that from Australia closest to an isolate from Denmark (divergence 0.003 ud/s).
Peanut mottle virus (PeMV) occurs worldwide and is a major pathogen of peanuts and soybeans, and of peas and common beans in Australia [36]. The cCP sequence of one isolate from Queensland has been determined (X73422) and was found to be closely related (mean divergence 0.025 ud/s) to cCPs of six isolates from the USA, which themselves have a mean divergence of 0.0197 ud/s. PeMV is a distinct species of potyvirus, but consistently pairs with yam mosaic virus (divergence 0.362 ud/s).
Candidatus Pleione virus Y (PlVY) is a distinct potyvirus known only from a gene sequence (AF185958) found in plants of Pleione spp. imported into a private Australian orchid collection [11]. PlVY was also found in several Pleione plants in an orchid collection at the Royal Botanic Gardens, Kew, U.K; Pleione spp. are prized bulbous orchids, mostly collected from the wild in southern China.
Potato virus Y (PVY), the type species of the genus Potyvirus, probably first entered Australia when seed potatoes were imported by Europeans. All isolates found in Australia are biologically indistinguishable from those found in other parts of the world [6]. The partial cCP sequences of three different Australian isolates have been determined (Brendan Rodoni, personal communication). These have divergences of 0.01-0.03 ud/s from the homologous region of the genomes of common European isolates. All the PVY cCPs available in Genbank form a monophyletic cluster within the PVY lineage, all members of which have been isolated from plants in the Americas, and most from species of Solanaceae growing in South America. PVY has a worldwide distribution, however it is probable that, like other members of the PVY lineage, it originated, as a species, in the Americas and has been traded around the world since the late 15th century in infected seed potatoes. There is no correlation between the phylogeny of different PVY isolates and their origins; all lineages contain isolates from all continents indicating that there has probably been much trading with infected tubers.
Candidatus Pterostylis virus Y (PtVY) was isolated from five genera of terrestrial Australian orchids (Pterostylis, Chiloglottis, Diurus, Eriochilus and Corybas) in private and public collections [11]. The cCP sequence of two isolates one from Pterostylis and the other Eriochilus (AF185964-5) differ from one another by 0.011 ud/s, but have divergences of around 0.13 ud/s with the closest known OrMV cCPs (AB079647/8/9). Isolates of OrMV (see above) are very diverse and have inter-isolate cCP divergences of up to 0.19 ud/s suggesting that OrMV may be a species complex. We do not know whether PtVY occurs in the wild in Australia, or whether the orchids from which it was recovered had become infected from other plants growing in the same collections.
Candidatus Rhopalanthe virus Y (RhVY) is known only from a gene sequence isolated from an orchid, Dendrobium philippinense (Dendrobium sect Rhopalanthe), imported into Australia (AF185956) [11]. The gene sequence databases contain only two cCPs more closely related to the RhVY cCP than those of the outgroup potyviruses, and both are from orchids; calanthe mild mosaic virus from Japan (AB011404; divergence 0.26 ud/s), and the partial cCP of a Cymbidium potyvirus from India (AJ871476).
Candidatus Sarcochilus virus Y (SarVY) is known only from gene sequences obtained from mottled plants of a lithophytic orchid of the genus Sarcochilus (AF185956) [11]. Sarcochilus is a genus of Australian orchids, but the virus was isolated from a plant in an orchid collection, and so it is uncertain whether the virus came from the wild in Australia, or from other plants in the collection. However the SaVY cCP sequence is closest to that of Eustrephus virusY (divergence 0.175 ud/s) (Fig 7) indicating that it is another member of the BCMV lineage, and probably Australian .
Candidatus Siratro 1 virus Y (Sir1VY) and Candidatus Siratro 2 virus Y (Sir2VY) were isolated from plants of weed siratros (Macroptilium atropurpureum) showing clear mosaic symptoms and growing on waste ground in Townsville, Queensland. The two cCP sequences, DQ098900 and DQ098901 respectively, differ from one another by 0.189 ud/s, but form a sublineage of the BCMV lineage that differs from its other members (Fig 7), such as peanut stripe virus, by 0.257 ud/s +/- 0.021 ud/s. It is uncertain whether they should be considered separate species or different isolates of one.
Sugarcane mosaic virus (SCMV) has been reported from all the sugarcane growing areas of Australia. It is widely distributed throughout the world, naturally infects many different grass species, and can be transmitted experimentally to even more. A dozen cCP sequences of Australian isolates have been determined (AJ278405, AF006728 – 38, D00948). They form a close knit, polytomous and probably monophyletic, group with a mean divergence of 0.011 ud/s in one part of the star cluster formed by all known SCMVs, thus it is most likely that the Australian isolates were introduced to Australia on a single occasion, perhaps when sugarcane was imported in 1924 [6], and they are most closely related to isolates from Brazil, China, India and the USA (smallest divergence 0.015 ud/s). The most diverse SCMV cCPs differ from one another by around 0.138 ud/s, and they are clearly separated from the other viruses of the SCMV lineage, which are maize dwarf mosaic, Pennisetum mosaic and Sorghum mosaic, and which have inter-species divergences of around 0.18-0.20 ud/s (Fig 6). Johnson grass mosaic virus which was originally confused with SCMV lineage viruses is distinct, and differs from them by a mean divergence of 0.374 ud/s.
Sweet potato potyviruses. The first potyvirus of sweet potato to be characterised was named sweet potato feathery mottle virus (SPFMV). Many more are now known, and most of them form a complex and diverse cluster that includes SPFMV, and has been split into the EA, RC, O and C strains; strain C is the most distinct and clearly should be considered a separate species as its mean divergence from the other strains is 0.171 +/-0.006 ud/s, whereas the mean divergences of the cCPs of the other three strains is only 0.053 +/- 0.017 ud/s respectively. Still more distantly related are sweet potato virus Y and sweet potato virus G. The EA strain is found only in East Africa.

The sequences of the cCP genes of Australian isolates of SPVY (AM050884-88), SPFMV-C (AM050891-3, AJ781778-9) and SPFMV-RC (AJ781775-7, AM050889-90) have been reported and are closely similar to isolates from elsewhere (Table 1).

Sweet potato (Ipomoea batatus) has not been found in the wild [28]. Before long-distance maritime trade started in the late 15th century it was found only in Mexico, the West Indies, Central and South America and, surprisingly, in Polynesia and New Zealand, but not Europe, Africa, Asia or Australia. Columbus then took it to Spain and within a few years it had been carried on to Africa, Asia, the Philippines and eventually Australia. There is no phylogenetic evidence that the many potyviruses found in sweet potato are from the Americas, and the preponderance and diversity of SPFMV isolates from Africa, where sweet potato is a major crop, suggests that that some of the viruses may have been acquired there.
Turnip mosaic virus (TuMV) has been reported from most continents of the world. It is probably the most widespread and important virus infecting crop, ornamental, weed and wild species of the family Brassicaceae and it is also found in a wide range of other species, both mono- and dicotyledonous. In south eastern Australia TuMV is widespread in the common immigrant weed Hirschfeldia incana in which it causes necrotic and chlorotic mosaic symptoms. The cCPs of two isolates (AF228514; AF226846) from this plant differ from one another by 0.016 ud/s, and are members of the world B lineage of TuMVs [26, 39] clustering closely with isolates from Africa, Asia, North America and New Zealand. The other Australian cCP (AB076543) came from an isolate from a crop of rocket (Eruca sativa) (Len Tesoriero, personal communication) and has a mean divergence from the Hirschfeldia incana isolates of 0.095ud/s; it is a member of the more diverse basal-B lineage of TuMVs [26, 39] and probably the first member of this TuMV lineage to have been found outside Europe.
Watermelon mosaic virus (WMV), formerly known as watermelon mosaic virus 2, is one of the most cosmopolitan potyviruses of cucurbit crops [5] and infects not only those that originated in the Old World, but also those that originated in the New World (see below). The single cCP sequence of WMV from Australia (D00535) [9] is most closely related (divergence 0.0014 ud/s) to that of an isolate from France. The cCPs of more than 50 isolates from different parts of the world population have been sequenced, and have divergences around 0.048 ud/s +/- 0.0076 ud/s. WMV is a member of the BCMV lineage.
Zucchini yellow mosaic virus (ZYMV) is another cosmopolitan virus widespread in cucurbit crops. It has been shown to be seed-borne [38], and this is probably the reason it is so widely dispersed. It has been isolated from all the important crop cucurbits that originated in the Old World, such as Benincasa hispida (wax gourd), Citrullus lanatus (watermelon), Cucumis melo (melon), Cucumis sativus (cucumber), Lagenaria siceraria (calabash gourd), Luffa spp. (loofah), Momordica charantia (bitter gourd), and also those that originated in the New World, namely the Cucurbita spp. that produce marrows, pumpkins, squash and zucchini.

ZYMV is widespread in Australian cucurbit crops [6]. Partial cCP gene sequences from four isolates have been reported [37], and are closely similar to those from other parts of the world (divergences less than 0.002 ud/s) (Fig 7).


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