Table 3 PhytoPipe analyses results for RNA-seq samples with confirmed pathogen infection
From: PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data
Sample ID/accession | Host plant | Confirmed pathogen infection | PhytoPipe detection | Taxon Observed in PhytoPipe | Contig numbers | Longest contig size | Kraken2 classified read number |
|---|---|---|---|---|---|---|---|
SRR5100668 | Solanum tuberosum (potato) | Ca. Liberibacter solanacearum (bacterium) | No | NA | NA | NA | NA |
SRR10148792 | Citrus sinensis (orange) | Ca. Liberibacter asiaticus (bacterium) | Yes | Candidatus Liberibacter asiaticus | 6 | 1799 | 235 |
SRR8295844 | Citrus sinensis (orange) | Ca. Liberibacter asiaticus (bacterium) | Yes | Candidatus Liberibacter asiaticus | 4 | 743 | 1289 |
SRR9225242 | Solanum lycopersicum (tomato) | Ca. Phytoplasma solani (bacterium) | Yes | Candidatus Phytoplasma solani | 466 | 10625 | 111578 |
SRR7186379 | Glycine max (soybean) | Ca. Phytoplasma sp. (bacterium) | Yes (different species) | 'Parthenium hysterophorus' phyllody phytoplasma | 502 | 4541 | 23497 |
SRR17253894 | Prunus pseudocerasus (Chinese cherry) | Ca. Phytoplasma sp. (bacterium) | Yes (different species) | Candidatus Phytoplasma ziziphi | 13 | 3154 | 76 |
SRR8003868 | Solanum sisymbriifolium (sticky nightshade) | Verticillium dahliae (fungus) | Yes | Verticillium dahliae | 19 | 3114 | 235401 |
Verticillium dahliae VdLs.17 | 15357 | 7370 | 23971 | ||||
Verticillium dahliae JR2 | 446 | 4269 | 1159 | ||||
SRR6760520 | Olea europaea (olive) | Verticillium dahliae (fungus) | Yes | Verticillium dahliae | 33 | 3819 | 1138562 |
Verticillium dahliae VdLs.17 | 15413 | 8672 | 109293 | ||||
Verticillium dahliae JR2 | 489 | 17964 | 4196 | ||||
SRR1525437 | Olea europaea (olive) | Verticillium dahliae (fungus) | Yes | Verticillium dahliae VdLs.17 | 8 | 382 | 46 |
SRR6053344 | Gossypium hirsutum (upland cotton) | Verticillium dahliae (fungus) | Yes | Verticillium dahliae | 54 | 3908 | 282087 |
Verticillium dahliae VdLs.17 | 15192 | 5044 | 26609 | ||||
Verticillium dahliae JR2 | 394 | 4307 | 1320 | ||||
SRR7814393 | Malus domestica (apple) | Erwinia amylovora (bacterium) | No | NA | NA | NA | NA |
SRR13488408 | Capsicum annuum (pepper) | Xanthomonas campestris pv. Vesicatoria (bacterium) | Yes (different species) | Xanthomonas euvesicatoria | 2 | 2417 | 6 |
ERR2036424 | Triticum aestivum (wheat) | Xanthomonas translucens (bacterium) | No | NA | NA | NA | NA |
ILVO_Cpnnyn (SRR24305225) | Chrysanthemum × morifolium (florist’s daisy) | Puccinia horiana (fungus) | Yes | Puccinia triticina | 105 | 1976 | 1010 |
Puccinia graminis f. sp. tritici CRL 75–36-700–3 | 115 | 1362 | 265 | ||||
Puccinia striiformis f. sp. tritici | 63 | 875 | 177 | ||||
ILVO_Salix (SRR24305224) | Salix alba (white willow) | Xylella fastidiosa (bacterium) | No | NA | NA | NA | NA |
ILVO_Daucu (SRR24305223) | Daucus carota (carrot) | Ca. Phytoplasma asteris (bacterium) | Yes (different species) | Aster yellows witches'-broom phytoplasma AYWB | 26 | 2087 | 2694 |
AGS_feve (SRR24305222) | Vicia faba (broad bean) | Ca. Phytoplasma sp. Flavescence dorée (bacterium) | Yes (different species) | Candidatus Phytoplasma vitis | 77 | 2739 | 1556 |
AGS_vigne (SRR24305220) | Vitis vinifera (grapevine) | downy mildew (fungus) | Yes (different species) | Plasmopara viticola | 270 | 3687 | 40052 |
KIS_V3417 (SRR24305219) | Daucus carota (carrot) | Alternaria sp. (fungus) | Yes (different species) | Alternaria solani | 3147 | 2442 | 38972 |
KIS_V3418 (SRR24305218) | Solanum tuberosum (potato) | Alternaria sp. (fungus) | Yes (different species) | Alternaria solani | 298 | 911 | 4760 |
KIS_V3408 (SRR24305221) | Solanum lycopersicum (tomato) | Phytophthora infestans (oomycete) | Yes | Phytophthora infestans | 25 | 2215 | 1265 |
Phytophthora infestans T30-4 | 92 | 575 | 1062 | ||||
KIS_V3408dup (SRR24305217) | Solanum lycopersicum (tomato) | Phytophthora infestans (oomycete) | Yes | Phytophthora infestans | 103 | 2739 | 9963 |
Phytophthora infestans T30-4 | 1920 | 2857 | 19252 |