Table 1.
Summary of Pratylenchus penetrans gene transcripts with known annotation selected for in situ hybridization assays.
| Tylenchida | Aph. | Rhab. | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P. penetrans | Pratylenchidae | RKN | Cyst | Ang. | |||||||||||||||
| Transcript code | Gland dataset (n = 22) | In planta dataset (n = 33) | Pc | Pz | Pt | Pv | Rs | Mi | Mh | Gp | Gr | Dd | Bx | Ce | ANNOTATION – NR database | Top‐hit species | blast top hit e‐value | blast top hit score | Accession |
| Homologues of known effector or gene candidates with relevant annotation | |||||||||||||||||||
| Ppen15842_c0_seq1 | Yes | Yes | + | + | – | + | + | + | + | + | + | + | – | – | β‐1,4‐Endoglucanase | Pratylenchus penetrans | 0.00E+00 | 909.83 | BAB68522.1 |
| Ppen15605_c0_seq1 | – | Yes | + | + | – | + | + | + | + | + | + | + | – | – | β‐1,4‐Endoglucanase | Pratylenchus goodeyi | 3.00E‐165 | 478.79 | AJD14760.1 |
| Ppen16218_c0_seq1 | Yes | Yes | + | + | + | + | + | + | + | + | + | + | – | – | β‐1,4‐Endoglucanase | Pratylenchus coffeae | 1.90E‐88 | 289.66 | ABX79356.1 |
| Ppen13447_c0_seq1 | Yes | Yes | + | + | + | – | – | + | + | + | + | + | + | – | Pectate lyase | Heterodera glycines | 1.30E‐84 | 265.77 | ADW77534.1 |
| Ppen14256_c0_seq1 | Yes | Yes | + | – | – | – | – | + | + | + | + | + | + | – | Pectate lyase | Globodera pallida | 9.70E‐52 | 181.80 | AEA08853.1 |
| Ppen12533_c0_seq1 | Yes | Yes | + | + | – | + | – | + | + | + | + | + | + | – | Expansin‐like | Heterodera avenae | 2.20E‐40 | 150.21 | APC23320.1 |
| Ppen15554_c1_seq1 | Yes | Yes | + | + | – | + | + | + | + | + | + | + | + | – | Expansin‐like | Heterodera glycines | 1.90E‐60 | 207.61 | ADL29728.1 |
| Ppen9511_c0_seq1 | – | Yes | + | + | – | + | + | + | + | + | + | + | + | – | Expansin‐like | Heterodera glycines | 1.80E‐62 | 213.00 | ADL29728.1 |
| Ppen18759_c0_seq1 | Yes | Yes | + | – | – | – | – | – | – | + | + | – | – | – | Arabinogalactan endo‐1,4‐β‐galactosidase | Heterodera schachtii | 4.10E‐123 | 359.00 | ACY02855.1 |
| Ppen12597_c1_seq1 | Yes | Yes | + | + | – | – | + | + | + | – | – | – | – | – | Glucuronoarabinoxylan endo‐1,4‐β‐xylanase | Radopholus similis | 0.00E+00 | 549.67 | ABZ78968.1 |
| Ppen15229_c0_seq1 | Yes | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Calreticulin | Pratylenchus goodeyi | 0.00E+00 | 638.26 | AIW66697.1 |
| Ppen11632_c0_seq1 | Yes | Yes | + | + | + | + | – | + | + | + | + | + | + | + | Venom allergen | Globodera rostochiensis | 4.00E‐84 | 261.54 | AEL16453.1 |
| Ppen9526_c1_seq1 | – | Yes | + | + | + | – | – | + | + | + | + | + | + | + | Venom allergen | Globodera rostochiensis | 1.50E‐34 | 139.42 | AEL16453.1 |
| Ppen16493_c0_seq1 | Yes | Yes | + | + | – | + | – | + | + | + | + | + | + | + | Catalase | Ditylenchus destructor | 0 | 623.21 | AFJ15102.1 |
| Ppen16592_c0_seq1 | – | Yes | + | + | – | + | + | + | + | + | + | + | + | + | Glutathione peroxidase | Globodera rostochiensis | 5.10E‐137 | 399.44 | AHW98769.1 |
| Ppen14407_c0_seq1 | Yes | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Transthyretin‐like family | Radopholus similis | 1.80E‐81 | 250.75 | CAM84513.1 |
| Ppen11355_c0_seq1 | Yes | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Transthyretin‐like family | Ancylostoma duodenale | 3.90E‐61 | 197.98 | KIH61588.1 |
| Ppen12000_c0_seq1 | Yes | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Transthyretin‐like family | Ancylostoma duodenale | 1.20E‐60 | 196.82 | KIH61588.1 |
| Ppen14007_c0_seq1 | – | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Transthyretin‐like family | Meloidogyne javanica | 2.10E‐76 | 237.27 | AKU46811.1 |
| Ppen12895_c0_seq1 | – | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Fatty acid‐ and retinol‐binding protein | Pratylenchus penetrans | 6.00E‐27 | 112.46 | APT68073.1 |
| Ppen11068_c0_seq1 | – | Yes | + | + | – | + | + | + | + | + | + | + | + | + | Fatty acid‐ and retinol‐binding protein | Aphelenchoides besseyi | 1.20E‐48 | 168.70 | AOC59163.1 |
| Ppen12103_c0_seq1 | – | Yes | + | + | + | + | + | + | + | + | + | + | – | + | SXP RAL‐2 protein | Meloidogyne incognita | 1.20E‐44 | 159.46 | AAR35032.1 |
| Proteases and inhibitor proteases | |||||||||||||||||||
| Ppen15235_c0_seq1 | Yes | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Cathepsin L‐like cysteine protease | Ditylenchus destructor | 3.80E‐156 | 459.14 | ACT35690.1 |
| Ppen14741_c0_seq1 | – | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Cathepsin L | Ancylostoma ceylanicum | 3.00E‐90 | 287.73 | EYC42688.1 |
| Ppen15220_c0_seq1 | Yes | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Protein BMA‐NPA‐1 | Brugia malayi | 6.60E‐89 | 314.69 | CRZ25179.1 |
| Ppen16129_c0_seq1 | – | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Cysteine protease precursor | Onchocerca volvulus | 1.80E‐143 | 420.62 | AAC47348.1 |
| Ppen13948_c0_seq1 | – | Yes | + | + | + | + | + | + | + | + | + | + | + | + | Papain family cysteine protease | Oesophagostomum dentatum | 3.00E‐76 | 253.00 | KHJ95394.1 |
| Ppen16494_c0_seq1 | Yes | Yes | + | + | – | + | + | + | + | + | + | + | + | + | Fatty acid amide hydrolase | Strongyloides ratti | 1.80E‐94 | 312.38 | CEF68470.1 |
| Ppen16868_c0_seq1 | Yes | Yes | + | + | – | + | + | + | + | + | + | + | + | + | Aspartyl protease | Meloidogyne incognita | 0.00E+00 | 690.26 | ABC88426.1 |
| Ppen15876_c0_seq1 | Yes | Yes | + | – | – | – | + | + | + | + | + | + | + | – | Trypsin‐like serine protease | Heliconius melpomene | 5.10E‐17 | 90.12 | ADJ58583.1 |
| Ppen12385_c0_seq1 | Yes | Yes | + | – | – | – | – | – | + | + | – | – | + | – | Serine protease | Caligus rogercresseyi | 5.30E‐12 | 75.49 | ACO10196.1 |
| Ppen13849_c0_seq1 | Yes | Yes | + | – | – | + | – | + | + | – | – | + | + | + | Trypsin inhibitor‐like cysteine‐rich domain protein | Dictyocaulus viviparus | 6.10E‐12 | 70.86 | KJH50180.1 |
| Ppen11515_c0_seq1 | Yes | Yes | + | – | – | – | – | – | – | – | – | – | – | – | Trypsin inhibitor‐like cysteine‐rich domain protein | Necator americanus | 6.30E‐09 | 65.08 | ETN72713.1 |
blast searches were performed against sequences in the non‐redundant (NR) database at the National Center for Biotechnology Information (NCBI) for a putative annotation, and against specific nematode proteins or transcriptome datasets for the presence/absence of positive blast hits (e‐value cutoff of 1e‐5 and bitscore > 50) in the corresponding species.
Ang., Anguinidae; Aph., Aphelenchida; Bx, Bursaphelenchus xylophilus; Ce, Caenorhabditis elegans; Cyst, cyst nematodes (Heteroderidae); Dd, Ditylenchus destructor; Gp, Globodera pallida; Gr, G. rostochiensis; Mh, Meloidogyne hapla; Mi, M. incognita; Pc, Pratylenchus coffeae; Pt, P. thornei; Pv, P. vulnus; Pz, P. zeae; Rhab., Rhabditida; RKN, root‐knot nematode (Meloidogynidae); Rs, Radopholus similis.