TABLE 3.
Summary of most relevant P. brassicae effector candidates.
| Gene ID | Annotation | Expression1 | Functional validation2 | Phenotype of homologous gene after mutation3 | Putative role in breaking resistance | Gene present in other P. brassicae isolates4 |
| SPQ95221.1 | Hypothetical protein | Upregulated in BR at 14 dai and in LA at 21 dai | N/A | N/A | Unknown | Pb3 (99%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPR00984.1 | Hypothetical protein | Upregulated in LA at 21 dai | N/A | N/A | Unknown | Pb3 (99%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ99629.1 | 30s ribosomal subunit 19 | Upregulated in LA at 21 dai | N/A | N/A | Unknown | Pb3 (88% – 142 nucleotides unaligned), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ98385.1 | E3 ubiquitin-protein ligase RING subunit | Upregulated in LA at 21 dai | N/A | N/A | Target host receptors for degradation (Yu et al., 2019) | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ96771.1 | S-phase kinase-associated protein 1 | Upregulated in LA at 21 dai | N/A | N/A | Ubiquitination and degradation (Mena et al., 2020) | Pb3 (97%), Pb_eH (99%), Pb_ZJ-1 (100%) |
| SPQ93076.1 | Benzoic acid/salicylic acid methyltransferase | High expression at 14 and 21 dai in both genotypes | Yes | N/A | Methylation of SA impairing plant response during clubroot disease (Ludwig-Müller et al., 2015), overexpression causes increases susceptibility to clubroot (Bulman et al., 2019; Djavaheri et al., 2019) | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPR00473.1 | Heat shock protein 70 | High expression at 14 and 21 dai in both genotypes | N/A | Reduced virulence | Aids in trafficking and processing of secreted pathogen proteins from P. falciparum and Magnaporthe oryzae (Yi et al., 2009; Shonhai, 2010) | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ96353.1 | Peptide methionine sulfoxide reductase | High expression at 14 and 21 dai in both genotypes | N/A | N/A | Catalyzes the reduction of oxidized methionine back to methionine (Weissbach et al., 2002), and therefore potentially aids in protection of pathogen proteins from ROS (El Hassouni et al., 1999) | Pb3 (100% – 19 nucleotides unaligned), Pb_eH (100% – 19 nucleotides unaligned), Pb_ZJ-1 (100% – 19 nucleotides unaligned) |
| SPQ99289.1 | Hypothetical protein | Upregulated in LA at 21 dai | N/A | N/A | Unknown | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPR01261.1 | Serine carboxypeptidase | Higher expression in BR at 14 dai and in LA at 21 dai | N/A | Reduced virulence | Resting spore germination (Feng et al., 2010) | Pb3 (99%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPR01202.1 | Stefin B | Higher expression in BR at 14 and 21 dai | N/A | N/A | Protease inhibitor against host proteases (Gumtow et al., 2018) | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ95766.1 | Protein kinase | Higher expression in BR at 14 dai and in LA at 21 dai | Yes | N/A | Potentially affecting cell cycle progression (Pérez-López et al., 2020) | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ97184.1 | Protein kinase | Upregulated in LA at 21 dai | N/A | Loss of pathogenicity | Germination, appressorium formation and infectious growth in Colletotrichum lagenarium (Yamauchi et al., 2004) | Pb3 (99% – 46 nucleotides unaligned), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ97185.1 | Protein kinase | Upregulated in LA at 21 dai | N/A | Loss of pathogenicity | Germination, appressorium formation and infectious growth in C. lagenarium (Yamauchi et al., 2004) | Pb3 (99%), Pb_eH (100%), Pb_ZJ-1 (100%) |
| SPQ95942.1 | Thioredoxin-like/glucosyltransferase 24 | Low expression (TPM < 100) at 14 and 21 dai in both genotypes | N/A | Reduced virulence | Cell wall/appressorium rigidity (Oliveira-Garcia and Deising, 2016) | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (98%) |
| SPQ99747.1 | Methyltransferase | Higher expression in LA at 21 dai | N/A | Reduced virulence | The arginine methyltransferase from F. graminearum methylates ribonucleoprotein complexes exported from the nucleus to the cytoplasm for mRNA maturation (Wang et al., 2012) | Pb3 (99%), Pb_eH (100%), Pb_ZJ-1 (99%) |
| SPQ96145.1 | Indole-3-acetaldehyde dehydrogenase | Low expression (TPM < 100) at 21 dai in both genotypes, and no expression detected at 14 dai | N/A | Reduced virulence | Synthesis of the auxin IAA by P. syringae (McClerklin et al., 2017). Increases of auxin during P. brassicae infection are central to disease development. | Pb3 (100%), Pb_eH (100%), Pb_ZJ-1 (100%) |
1Upregulation refers to a significant difference in expression. Expression values can be seen in Table 1 and Supplementary Table 6.
2Functional validation in the context of the clubroot pathosystem.
3Refers to the comparison made with PHI-base in Table 2.
4Genome isolates correspond to pathotypes Pb3 (Rolfe et al., 2016), ZJ-1 (Bi et al., 2019), and eH (Daval et al., 2019). Unaligned nucleotides correspond to regions from the query without a High-Scoring Pair (HSP), during BLAST analysis.