2.9 | Gene content in the candidate genomic regions
The annotated reference genome of P. fijiensis was used to
identify all the genes in all the genomic regions detected using the
genome scan approaches and that were putatively involved in the host
adaptation. The annotation (Go terms, KOG terms, and presence of a
peptide signal) for these genes was retrieved from the GGF3 file of the
JGI website
(https://genome.jgi.doe.gov/Mycfi2/Mycfi2.home.html). We
also tested whether these genes corresponded to in silico defined
SSPs (Arango Isaza et
al., 2016) or to proteins secreted in vitro and in plantaby comparing isolates with different pathogenicity levels
(Escobar-Tovar et al.,
2015) or genes expressed during infection in a transcriptome analysis
(Noar & Daub, 2016).
Protein sequences were subjected to a BLAST
(Altschul et al.,
1990) search in the pathogen-host interactions database (PHI-base,
version 4.9), which currently contains around 6 000 genes proven to
affect the outcome of host-pathogen interactions
(Urban et al., 2015).
For each BLAST search, we kept the gene in the PHI-base that had the
lowest bitscore (and E value < 1x10-9) and
an effect on quantitative pathogenicity (i.e. phenotype “loss of
pathogenicity”, “reduced virulence”, “increased virulence”).