11
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 (http://www.anbg.gov.au/cpbr/databases/apni-search-full.html), 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).