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Table 1 List of isolates used in this study

From: Real-time loop-mediated isothermal amplification: an early-warning tool for quarantine plant pathogen detection

Species Isolate code Groupb Host Origin Collectorc Molecular assayd
LAMPe qPCRf
tamp (min:s) Ta (°C) Detection
X. fastidiosa assay
 Xylella fastidiosa subsp. pauca Co.Di.Roa T Olea europaea Italy M. Saponari 7:15 88.98 +
 Xylella fastidiosa subsp. fastidiosa Xffa T Prunus dulcis USA J. Chen 14:20 88.78 +
 Xylella fastidiosa subsp. multiplex Xfma T Liquidambar styraciflua USA S. Russell 7:00 88.83 +
 Pseudomonas savastanoi pv. savastanoi ITM05a CHC Olea europea Italy G. Marchi
 Pantoea agglomerans PaFL1a CHC Olea europea Italy G. Marchi
 Pseudomonas fluorescens KL218a CHC Actinidia deliciosa Italy G. Marchi
 Xanthomonas arboricola pv. pruni Xap PR Prunus laurocerasus Italy A. Raio
 Pseudomonas savastanoi pv. nerii Ps.sav CHC Nerium oleander Italy A. Raio
 Pseudomonas koreensis KL217a NP, O Actinidia deliciosa Italy G. Marchi
 Pseudomonas syringae KL34a O Actinidia deliciosa Italy G. Marchi
 Pseudomonas syringae KL32a O Actinidia deliciosa Italy G. Marchi
 Pseudomonas viridiflava KL24a O Actinidia deliciosa Italy G. Marchi
 Pseudomonas mediterranea C5P1rad1a O Chrysanthemum sp. Italy M. Fiori
 Pseudomonas corrugata C2P1 rada O Chrysanthemum sp. Italy M. Fiori
 Pseudomonas syringae pv. photiniae CFBP2899a O Photinia glabra Japan CFBP
 Pectobacterium carotovorum C24a O Zantedeschia aethiopica Italy G. Marchi
 Pectobacterium carotovorum C6a O Zantedeschia aethiopica Italy G. Marchi
 Pantoea agglomerans pv. gypsophilae Ehg824-1a O Gypsophila paniculata Israel G. Marchi
 Pseudomonas syringae pv. actinidiae KL103a O Actinidia deliciosa Italy G. Marchi
 Pseudomonas syringae pv. tabaci GSPB1209a O Nicotiana sp. Italy G. Marchi
 Pseudomonas syringae pv. viburni CFBP1702a O Viburnum sp. USA CFBP
 Sphingomonas sp. KVPT7FAa NP, CHC Actinidia deliciosa Italy G. Marchi
 Stenotrophomonas malthopylia St NP, PR Capsicum annum Italy A. Raio
 Xanthomonas campestris pv. campestris Xcc PR Brassica spp. Italy A. Raio
 Xanthomonas arboricola pv. juglandis Xaj PR Juglans regia Italy A. Raio
 Erwinia amylovora Ea12 O Pyrus communis Italy C. Cainelli
 Agrobacterium tumefaciens LMG37 O Prunus spp. USA BCCM/LMG
 Agrobacterium vitis CFBP5523 O Vitis vinifera Australia CFBP
C. platani assay
 Ceratocystis platani CBS117355 T Platanus sp. France CBS-KNAW 10:08 88.14 +
 Ceratocystis platani Cp3 T Platanus × acerifolia Italy IPSP-CNR 12:15 88.55 +
 Ceratocystis platani Cp6 T Platanus × acerifolia Italy IPSP-CNR 9:08 88.30 +
 Ceratocystis platani G160 T Platanus × acerifolia Turkey T. Dogmus 16:58 88.93 +
 Ceratocystis platani DB203 T Platanus × acerifolia Turkey T. Dogmus 14:08 88.78 +
 Ceratocystis platani CBS115162 T Platanus occidentalis USA CBS-KNAW 8:00 88.83 +
 Ceratocystis platani Cp24 T Platanus × acerifolia Italy IPSP-CNR 8:00 88.43 +
 Ceratocystis fimbriata CBS 115167 PR Syngonium sp. USA CBS-KNAW 10:05 88.45
 Ceratocystis fimbriata CBS 118126 PR Syzgium aromaticum Sulawesi CBS-KNAW 15:10 88.70
 Ceratocystis fimbriata CBS 115175 PR Mangifera indica Brazil CBS-KNAW 9:30 88.20
 Ceratocystis fimbriata CBS 115174 PR Eucalyptus sp. Brazil CBS-KNAW 14:00 88.50
 Ceratocystis fimbriata CBS 115171 PR Colocasia esculenta Brazil CBS-KNAW 10:13 88.60
 Ceratocystis fimbriata CBS 74040 PR Crotolaria juncea Brazil CBS-KNAW 13:38 88.00
 Sarcodontia pachyodon Sp5 O, CHC Platanus × acerifolia Italy IPSP-CNR
P. ramorum assay
 Phytophthora ramorum Prama T Rhododendron sp. Greece P. Tsopelas 7:58 88.68 +
 P. ramorum LSVM123a T Rhododendron sp. France R. Ioos-N. Schenck 7:07 88.48 +
 P. ramorum LSVM362a T Rhododendron sp. France R. Ioos-N. Schenck 6:15 88.73 +
 P. ramorum LSVM386a T Rhododendron sp. France R. Ioos-N. Schenck 6:72 88.68 +
 P. ramorum LSVM390a T Rhododendron sp. France R. Ioos-N. Schenck 7:00 88.53 +
 P. ramorum LSVM391a T Leucothoe sp. France R. Ioos-N. Schenck 6:30 88.53 +
 P. ramorum LSVM401a T Rhododendron sp. France R. Ioos-N. Schenck 7:07 88.53 +
 P. ramorum LSVM402a T Rhododendron sp. France R. Ioos-N. Schenck 7:00 88.53 +
 P. ramorum LSVM405a T Rhododendron sp. France R. Ioos-N. Schenck 7:15 88.48 +
 P. lateralis Plata PR Chamaecyparis lawsoniana France C. Robin 9:00 88.43 +
 P. alni subsp. uniformis Ph68 PR Alnus cordata Italy G. P. Barzanti 23:27 90.47
 P. cactorum PCA1a PR Aesculus hippocastanum Germany J. Schumacher
 P. × cambivora Ph21a PR Castanea sativa Italy A. Vettraino 25:22 90.67
 P. cinnamomi 28SA PR Laurus nobilis Italy IPSP-CNR 16:37 89.62
 P. cinnamomi Ncfca PR Unknown Italy IPSP-CNR
 P. cryptogea 13SA PR Prunus laurocerasus Italy IPSP-CNR 22:07 89.78
 P. citricola 51RC PR Viburnum lucidum Italy IPSP-CNR
 P. citricola Pcl1a PR Unknown Germany T. Jung 27:27 89.82
 P. citrophthora 33SB PR Euonymus spp. Italy IPSP-CNR 20:05 89.23
 P. citrophthora Ph9a PR Convolvolus sp. Italy S. O. Cacciola 18:15 89.58
 P. europaea PE1a PR Unknown Germany T. Jung 15:12 90.42
 P. foliorum 2015–1454a PR, CHC Rhododendron UK A. Pérez-Sierra 11:15 89.08
 P. gonapodyides PG7a PR Quercus robur Germany S. Leonhard
 P. gonapodyides IHTM PR Alnus cordata Italy IPSP-CNR
 P. megasperma Ph78 PR Prunus avium Italy G. P. Barzanti
 P. megasperma PMIa PR Quercus robur Germany S. Leonhard
 P. nicotianae 1RB PR Myrtus communis Italy IPSP-CNR
 P. palmivora 44RC PR Prunus laurocerasus Italy IPSP-CNR
 P. quercina PQ4a PR Quercus robur Germany S. Leonhard/J. Schumacher
 P. syringae Psy2a PR Unknown Germany J. Schumacher 17:45 89.48
 Elongisporangium anandrum PYAa O Quercus robur Germany S. Leonhard
 Phytopythium litorale 40SB O Prunus laurocerasus Italy IPSP-CNR
 Elongisporangium undulatum 76SB O Cupressus sempervirens Italy IPSP-CNR
 Mortariella sp. 26RA O Arbutus unedo Italy IPSP-CNR
 Diplodia mutila Dm O Quercus spp. Italy IPSP-CNR
 D. pinea 128 O Pinus resinosa USA M. A. Palmer
 D. scrobiculata 124 O Pinus resinosa USA M. A. Palmer
 D. seriata UCD 352 O Vitis vinifera USA J. R. Urbez-Torres
 D. seriata WP-J10 O Vitis vinifera Australia S. Savocchia
 Geosmithia pallida IVV7 O Ulmus spp. Italy IPSP-CNR
 Ophiostoma novo ulmi subsp. americana HI72 O Ulmus spp. USA IPSP-CNR
  1. aSamples provided as DNA
  2. bFor each molecular assay developed in this study different groups of isolates were tested: target species (T); phylogenetically related species (PR), CHC = common host colonizers species (CHC); out-group species (O)
  3. cCBS Centraalbureau voor Schimmelcultures (CBS) Fungal Biodiversity Centre—Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands; CFBP French Collection of Plant Pathogenic Bacteria, INRA, France; IPSP-CNR Institute for Sustainable Plant Protection—National Research Council, Firenze, Italy; BCCM/LMG Bacteria Collection Laboratorium voor Microbiologie Universiteit Gent Bacteria Collection, Laboratorium voor Microbiologie, Universiteit Gent, Belgium
  4. dMolecular assays are referred to LAMP and qPCR described in Table 2
  5. etamp amplification time, Ta annealing temperature, – not detected
  6. f+ positive, − negative