3.5 | Gene content in the candidate genomic regions
A total of 118 genes distributed in 25/32 candidate regions were
identified using the annotated reference genome of P. fijiensis(Arango Isaza et al.,
2016). However, due to linkage disequilibrium and the hitchhiking
effects, it is unlikely that all these genes are involved in
pathogenicity and adaptation. The number of genes per region ranged from
1 to 12. All the information on these genes available to date is
provided in supplementary (Table S5). None of the candidate genes
corresponded to the putative small secreted proteins (SSPs) identifiedin silico in Arango-Isaza et al.
2016, which are
putative effectors involved in plant-pathogen interactions. However,
secreted molecules other than SSPs can also be effectors
(Rovenich et al.,
2014). We identified 10 genes distributed across nine regions with a
peptide signal that could correspond to effectors (Table 5). Only one
gene among these genes was identified in the in-vitro secretome
of P. fijiensis published by Escobar-Tovar et al.
2015. Four other genes
found in different regions were associated with increased expression in
leaf tissues infected by P. fijiensis in the transcriptome study
published by Noar & Daub
2016. Finally, we
found 17 genes distributed in 10 genomic regions corresponding to
homologous genes indexed in the PHI-base (a database containing more
than 6 000 genes involved in host-pathogen interactions, (Urban et al.,
2015)) that are known to lead to a total loss, reduction, or gain in
pathogenicity in other fungal species. A total of 12 genes located in
the 17 regions significantly correlated with DLA-R and/or DLA-S were
also identified in at least one of the other previous analyses. Based on
all the data available at present, we considered several genes as
candidates involved in quantitative pathogenicity and host adaptation
(highlighted in Table 5 and details in Table S5): three major candidate
genes (highlighted in red in Table 5 and Table S5) were located in
regions significantly correlated with DLA-R or DLA-S and previously
identified in at least two of the databases consulted, other good
candidates (highlighted in grey) were located in regions correlated to
DLA-S or DLA-R and identified in one of the database (9 genes) or found
in at least two of the databases consulted (4 genes).