De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms

Table 4 Gene family identification among predicted proteins from the grapevine phylloxera (transcriptome-based) and proteins from the pea aphid genome (official gene set, version 2.1), using OrthoMCL

	#families	#genes, pea aphid	#genes, phylloxera
Many to Many	137	988	379
Many (pea paphid) to one (phylloxera)	935	3438	935
Many (phylloxera) to one (pea paphid)	207	207	450
One to one	7103	7103	7103
Pea aphid specific families	3702	14,995	0
Phylloxera specific families	683	0	3047
Phylloxera specific singletons	-	-	5458
Pea aphid specific singletons	-	10,259	-
Total # genes per species	-	36,990	17,372

The first column precises the different categories of homology relationships: gene families may contain several copies in both species which are co-orthologs (“Many to Many”, all these genes being co-orthologs), several copies in one species ortholog to only one copy in the other species (“Many to one”), only one copy in each species (1:1 orthology, or “One to one”), or yet may contain copies in only one species (“Pea aphid-specific“ or “Phylloxera-specific”). Finally, genes from one species not found in gene families and without any ortholog in the other species are “Singletons”. The numbers of families of each type are given, along with the number of predicted genes from each species for each category

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