II.8" - Agrogenom clade-specific genes

Sets of clade-specific genes derived from the ancestral genome gene content estimations in Agrogenom database.
Procedure for detection of clade-specific genes from phylogenetic profiles:Clade-specific genes were defined as genes gained (or lost) by the clade ancestor and conserved (not re-gained) in all clade members since. We first identified genes marked by gain/loss events in the genome of a clade ancestor. Then, we identified clade-specific genes by searching for contrasting patterns in the phylogenetic profile of the presence or absence of each gained/lost gene. These profiles were established from the scenarios of orthologous subfamily evolution (see above and Supplementary Text, section 3, step 6). A background clade was chosen as the one corresponding to the next higher taxonomic unit (genus, species complex, etc.) in which the focal (foreground) clade was nested. Contrast was initially defined between the foreground and background clades, where foreground genomes had a consistently opposite pattern to that of genomes in the background clade. However, possible subsequent transfer or loss events in the background clade can blur the contrasting pattern in phylogenetic profiles. Clade-specific genotypes were thus identified using a relaxed definition of clade specificity, i.e. where the presence/absence contrast could be incomplete, with up to two genomes in the background clade sharing the foreground state.