Table 1.

Comparative gene-by-gene phylogenomic analysis and identified HGTs

Species	P. ramorum	P. sojae	P. infestans	H. parasitica
Total no. of predicted proteins	15,743	19,027	22,658	13,240
Total proteins used in phylogenetic analysis	6,871	6,079	7,093	3,365
No. of gene cluster groups used for phylogenetic analyses [after OrthoMCL (24) clustering]	3,014	3,018	3,233	2,169
No. of HGT gene families strongly supported by all methods	19	17	11	4
No. of “gray zone” HGT gene families (Table 2 and Table S3)	11	10	7	5
Total putative ORFs from fungal-derived HGTs	143	117	48	21
Total secreted proteins in genome identified by both WoLFPSORT and SignalP	1,326	1,586	1,123	411
Total no. of proteins analyzed with phylogeny predicted to be secreted	521	630	351	121
No. of fungal HGT-derived proteins with N-terminal secretion motif	101	89	30	13
% Total predicted secretome derived from fungi by HGT	7.61	5.61	2.67	3.16
% Proteins analyzed that are predicted to be secreted and are derived by HGT	19.38	14.13	8.55	10.74