Table 2.

Summary of support for each HGT and gene annotation in brief

HGT ID 1–34	GenBank accession no./Joint Genome Institute database protein ID	Support for HGT: phylogeny (P), bootstrap analysis (B), topology comparison tests (Ct), and/or taxon distribution (Td)	Conserved introns between donors and recipients (Table S4)	Annotation of putative function	Reported by Richards et al. (19)
1 (Fig. S1.1)	EEY57756	P, B, Ct, Td	1 shared intron	MFS transporters similar to saccharide monomer transporters	Yes (named AraJ)
2 (Fig. S1.2)	82760 (P. ramorum)	P, B, Ct		Extracellular esterase/lipase	Yes (named esterase/lipase (ref. 19, Fig. S3B)
3 (Fig. S1.3)	AAM48174.1	P, B, Ct		Aldose 1-epimerase	Yes (named GalM)
4 (Fig. S1.4)	71178 (P. ramorum)	P, B, Ct, Td		α-ketoglutarate dependent xanthine dioxygenase (XanA)
5 (Fig. S1.5)	EEY56552	P, B, Ct		Dehydrogenase/reductase family protein
6 (Fig. S1.6)	72257 (P. ramorum)	P, B, Ct, Td		Extracellular quercetin 2,3-dioxygenase
7 (Fig. S1.7)	EEY52979	P, B, AU test is borderline		Extracellular α-l-rhamnosidase (glycosyl hydrolase 78)
8 (Fig. S1.8)	EEY63463	P, B, Ct		Lactonohydrolase/gluconolactonase
9 (Fig. S1.9)	EEY64355	P, B, Ct		Extracellular glucooligosaccharide oxidase
10 (Fig. S1.10)	EEY59160	P, B, Ct		Extracellular unsaturated rhamnogalacturonyl hydrolase (glycosyl hydrolase 88)
11 (Fig. S1.11)	83543 (P. ramorum)	P, B, Ct		Transcription factor
12 (Fig. S1.12)	85044 (P. ramorum)	P, B, Ct, Td	1 shared intron	3-octaprenyl-4-hydroxybenzoate carboxy-lyase/Phenylphosphate carboxylase family
13 (Fig. S1.13)	EEY53137	P, B, Ct	1 shared intron	Phosphatidylinositol transfer protein
14 (Fig. S1.14)	133521 (P. sojae)	P, B, Ct		Extracellular protein similar to prokaryote lipases
15 (Fig. S1.15)	142730 (P. sojae)	P, B, Ct	1 shared intron	Esterase/lipase protein domain family
16 (Fig. S1.16)	EEY68514	P, B, Ct		Xylitol dehydrogenase/sorbitol dehydrogenase
17 (Fig. S1.17)	EEY55544	P, B, Ct, Td	2 shared introns	Extracellular arabinan-endo-1,5-α-l-arabinosidase (glycosyl hydrolase 43)
18 (Fig. S1.18)	EEY59913	P, B, Ct, Td		Transporter for purines and pyrimidines	Yes (named CodB)
19 (Fig. S1.19)	141189 (P. sojae)	P, B, Ct		Extracellular protein with an esterase/lipase domain
20 (Fig. S1.20)	EEY58144	P, B, Ct, Td		Putative member of the NPP1 (necrosis and ethylene-inducing peptide 1 proteins)
21 (Fig. S1.21)	EEY64154	P, B, Ct, Td	1 shared intron	Conserved hypothetical protein with similarity to a prokaryotic antibiotic biosynthesis monooxygenase
22 (Fig. S1.22)	EEY62062	P, Td		Pectate lyase
23 (Fig. S1.23)	EEY67135	P, Td		Extracellular intradiol dioxygenase	Yes (named PcaH)
24 (Fig. S1.24)	ABB22031	P, Td		Extracellular endoglucanase (glycosyl hydrolase 12)
25 (Fig. S1.25)	EEY67552	P, B	1 shared intron	Extracellular histidine phosphatase domain protein
26 (Fig. S1.26)	EEY65395	P, B	2 shared intron	Extracellular endo-1,4-β-xylanase (glycosyl hydrolase 10)
27 (Fig. S1.27)	75147 (P. ramorum)	P, B		Member of Zinc metalloprotease proteins which include archaemetzincin
28 (Fig. S1.28)	EEY56384	P, B		Extracellular arabinogalactan endo-1,4-β-galactosidase (glycosyl hydrolase 53)
29 (Fig. S1.29)	77558 (P. ramorum)	P, B		Aliphatic nitrilase (CN hydrolase family)
30 (Fig. S1.30)	EEY68947	P, Td		Extracellular α-l-rhamnosidase (glycosyl hydrolase 78)
31	76863 (P. ramorum)	Td		LysM domain protein
32	EEY55495	Td		Extracellular conserved hypothetical protein
33	134308 (P. sojae)	Td		NmrA, a negative transcriptional regulator
34	EEY58177	Td		Conserved hypothetical protein

Sequences for P. ramorum and P. sojae are available from the Department of Energy, Joint Genome Institute website. Protein sequences can be obtained using the protein ID and searching at http://genome.jgi-psf.org/pages/search-for-genes.jsf?organism=Phyra1_1 for P. ramorum and http://genome.jgi-psf.org/pages/search-for-genes.jsf?organism=Physo1_1 for P. sojae.