TABLE 4.
Putative functions and replicon location of genes associated with the EPC phenotypes in pea/lentil, identified by the comparative genomic analyses.
| Genomic location | ||||||||
|
|
||||||||
| Gene identifier | EPC component | Putative function | 3841 | Vaf10 | Vaf-108 | BIHB1217 | UPM791 | TOM |
| PK1 | CFN | hypothetical protein | NA | Rh08 | Rh08 | Rh08 | Rh08 | NA |
| PK2 | CFN | hypothetical protein | NA | NA | Rh02 | Rh02 | Rh02 | NA |
| PI1 | CFN | putative transmembrane | chr | NA | NA | chr | chr | NA |
| PI2 | CFN | putative transmembrane | chr | NA | NA | chr | chr | NA |
| PI3 | CFN | hypothetical protein | chr | chr | NA | chr | chr | NA |
| PI4 | CFN | RelE/StbE replicon stabilization toxin | chr | chr | NA | chr | chr | NA |
| PI5 | CFN | hypothetical protein | chr | NA | NA | chr | chr | NA |
| PI6 | CFN | amidinotransferase | chr | NA | NA | chr | chr | NA |
| PI7 | CFN | amidinotransferase | chr | NA | NA | chr | chr | NA |
| PI8 | CFN | miscellaneous | chr | NA | NA | chr | chr | NA |
| PI9 | CFN | putative transcriptional regulator | Rh03 | Rh08 | Rh01 | Rh08 | Rh08 | NA |
| PI10 | CFN | hypothetical protein | Rh03 | Rh08 | Rh01 | Rh08 | Rh08 | NA |
| PI11 | CFN | uracil/thymine DNA glycolase | Rh02 | NA | NA | Rh02 | Rh02 | NA |
| PI12 | CFN | L-2-hydroxyglutarate oxidase | Rh05 | NA | NA | Rh04a | Rh04a | NA |
| PI13 | CFN | L-proline/glycine betaine transporter ProP | Rh05 | NA | NA | Rh01 | Rh01 | NA |
| PA1 | CFN | hypothetical protein | NA | chr | chr | NA | NA | NA |
| PA2 | CFN | Delta-9 fatty acid desaturase | NA | chr | NA | NA | NA | NA |
| PA3 | CFN | Putative membrane-bound ClpP-class protease | chr | chr | chr | chr | chr | NA |
| PA4 | CFN | hypothetical protein | Rh02 | NA | Rh02 | Rh02 | Rh02 | NA |
| PA5 | CFN | hypothetical protein | chr | chr | chr | Rh01 | NA | NA |
| PA6 | CFN | hypothetical protein | NA | Rh08 | Rh17 | NA | NA | NA |
| LA1 | CFN | TPR domain protein in aerotolerance operon | chr | Rh12 | NA | chr | NA | NA |
| LA2 | CFN | BatA | chr | Rh12 | Rh01 | chr | NA | NA |
| LA3 | CFN | Possible Neuromedin U precursor | chr | Rh12 | NA | chr | NA | NA |
| LA4 | CFN | Enoyl-acyl-carrier-protein reductase | chr | NA | NA | NA | NA | NA |
| LA5 | CFN | hypothetical protein | Rh01 | Rh01 | NA | Rh01 | NA | Rh01 |
| LA6 | CFN | hypothetical protein | chr | NA | NA | chr | chr | NA |
| LR1 | CFN | Cell filamentation protein fic | chr | Rh08 | chr | chr | chr | NA |
| LR2 | CFN | VapC toxin protein antagonist | Rh01 | NA | Rh01 | NA | NA | Rh01 |
| LF1 | CFN | Polyhydroxyalkanoic acid synthase | Rh03 | Rh17 | Rh17 | Rh08 | NA | NA |
| LF2 | CFN | Acetyl-coenzyme A synthetase | Rh03 | Rh01 | NA | Rh08 | NA | NA |
| LF3 | CFN | Homoserine O-acetyltransferase | Rh03 | Rh01 | NA | Rh08 | NA | NA |
| LF4 | CFN | putative dehalogenase-hydrolase | Rh03 | Rh01 | NA | Rh08 | NA | NA |
| LF5 | CFN | hypothetical protein | Rh03 | Rh01 | Rh01 | Rh08 | NA | NA |
| LF6 | CFN | hypothetical protein | Rh03 | Rh01 | Rh01 | Rh08 | NA | NA |
| LF7 | CFN | hypothetical protein | Rh03 | Rh01 | NA | Rh08 | NA | NA |
| PAFN1 | AFN | hypothetical protein | NA | Rh01 | Rh01 | NA | NA | Rh01 |
| PAFN2 | AFN | MFS permease | chr | chr | chr | NA | NA | chr |
| PAFN3 | AFN | hypothetical protein | NA | NA | NA | NA | NA | chr |
| PAFN4 | AFN | Beta-galactosidase | chr | NA | chr | NA | NA | chr |
| PAFN5 | AFN | Beta-galactosidase | chr | NA | chr | NA | NA | chr |
| PAFN6 | AFN | CobN component of cobalt chelatase | chr | chr | NA | NA | NA | chr |
| PAFN7 | AFN | hypothetical protein | NA | Rh12 | NA | Rh06 | NA | Rh06 |
| PAFN8 | AFN | hypothetical protein | Rh12 | Rh12 | Rh01 | Rh06 | Rh12 | Rh06 |
| PAFN9 | AFN | Bll0066 protein | Rh12 | Rh12 | Rh01 | Rh06 | Rh12 | Rh06 |
| PAFN10 | AFN | hypothetical protein | Rh12 | Rh12 | Rh01 | Rh06 | Rh12 | Rh06 |
| PAFN11 | AFN | Probably methylase/helicase | Rh12 | Rh12 | Rh01 | Rh06 | NA | Rh06 |
| PAFN12 | AFN | nodT RND efflux system | Rh03 | Rh01 | Rh08 | Rh08 | NA | Rh06 |
| PAFN13 | AFN | Alpha-aspartyl dipeptidase Peptidase E | chr | chr | chr | NA | NA | chr |
| PAFN14 | AFN | putative transmembrane protein | chr | chr | chr | chr | chr | chr |
| PAFN15 | AFN | PE-PGRS FAMILY PROTEIN | chr | chr | NA | NA | NA | chr |
| PAFN16 | AFN | hypothetical protein | chr | chr | NA | NA | NA | chr |
| PAFN17 | AFN | Bll0066 protein | Rh12 | Rh12 | Rh01 | Rh06 | Rh12 | Rh03 |
Replicons are classified (‘chr’ chromosome or ‘rh’ type plasmid) based on sequence homology to repABC genes as described by Cavassim et al., 2020. NA indicates no significant homologous sequence. Gene identifiers referred to the host and the EPC component (CFN or AFN). Gene identified by comparing host-compatible bacteria displaying contrasted level of competitiveness were labelled as CFN and associated to the host used for the comparison: pea cv. ‘Kayanne’ (PK), pea cv. ’Isard’ (PI), pea cv. ‘Afghanistan’ (PA), lentil cv. ‘Anicia’ (LA), lentil cv. ‘Rosana’ (LR) and lentil cv. ‘Flora’ (LF). Gene identified by comparing Rlv strains displaying contrasted ability to form nodule with pea cv ‘Afghanistan’ were labelled AFN (PAFN). More details are provided in Supplementary Table 14.