Table 1.

Information of the 42 HGT orthogroups including the HGT recipient, donor, expression, D_n/D_s, functional category, and homology-based annotation

Ortho group	Recipient	Donor	Intron	Expression	Dn/Ds	Functional category	Annotation based on homology
226	P	Poptr	Y/Y	1, 4.2	P	Defense	Cytochrome P450
1685	P	Gyma + Medtr	Y/Y	>2	P	Defense	Cysteine-rich receptor-like kinase
2376	P	Poptr + Theca	Y/Y	>2	RP	Defense	Proteasome subunit alpha type
14624	S	Sorbi + Zea	N/N-5′UI	NA	P	Defense (disease resistance)	BTB/POZ
23343	P	Theca	—	5.2	P	Defense (disease resistance)	Disease resistance protein
11841	P	Frave	Y/Y	5.1	SP	Defense	Hyoscyamine 6-dioxygenase-like
1886	P	Frave	—	6.2	RP	Defense (immunity)	Ankyrin repeat family protein
11437	P	Frave	—	>2	RP	Defense and nodule development	Kelch modif related to galactose oxidase
8888	P	Frave	—	2, 4.1	RP	Transcription	Poly(A) polymerase
18709	P	Arath	Y/Y	Int	POS	Transcription	Nucleolin 2-like
806	P	Theca	Y/Y	Int	RP	Translation	Valyl-tRNA synthetase
2270	P, S	Theca	Y/Y	>2	RP	Translation	Methionyl-tRNA synthetase
4067	P	Frave	Y/Y	41	RP	Translation	tRNAHis guanylyltransferase
10050	P	Frave	—	42	RP	Translation	Histidine-tRNA ligase
13892	P	Medtr	Y/Y	Int	P	Translation	Ribosomal protein S13
17	P	Betvu	Y/Y	4.2, 5.1, 6.2	P	Nutrient transport	ABC transporter C family member 3
9613	P	Glyma	Y/Y	0	RP	Nodule development and cytokinin biosynthesis	Cytosolic purine 5-nucleotidase
15246	P	Medtr	—	6.2	P	Defense-related (insect toxin)	Albumin I (28)
1226	P	Poptr	Y/Y	3, int	RP	Diverse	Alpha/beta-Hydrolases
10143	P	Frave	—	4.2	RP	Diverse	Tubulin-specific chaperone D
3861	P + L	Glyma	Y/Y	>2	POS	Diverse	Poly(ADP ribose) glycohydrolase
4598	P	Medtr	—	Int	RP	Diverse	Nuclear pore complex protein
19696	P	Poptr	Y/Y	4.1, 6.2	SP	Diverse	Ubiquitin-like–specific protease 1
16703	S	Orysa	Y/Y	52	P	Diverse	Zinc finger, GRF-type
4572	P	Frave	—	3, 4.1	P	Diverse	FBD-associated F-box protein
5896	S	Glyma	Y/Y	5.2, 6.1	P	Plastid-to-nucleus signaling	Uroporphyrinogen-III synthase
218	P, S, T	Prunus	Y/Y (2)	>2	P	TE	hAT transposon
1021	P, T	Frave + Malus	Y/Y	>2	P	TE	hAT transposon
5002	P	Prunus	Y/Y	Int	P	TE	hAT transposon
12835	S	Sorbi	N/N	0	P	TE	Putative harbinger Transposase-derived nuclease
14230	P	Prunus	Y/Y	42	P	TE	MULE transposase
15149	P	Frave	Y/Y	Int	P	TE	hAT transposon
13512	P	Frave	—	51	POS	Unknown	Unknown
14233	S	Sorbi + Orysa	Y/Y	6.1	SP	Unknown	Unknown
14675	P	Frave	—	6.2	P	Unknown	Unknown
18354	P	Frave	—	Int	P	Unknown	Unknown
20190	P	Frave	—	int, 2	P	Unknown	Unknown
23480	P	Frave	—	Int	P	Unknown	Unknown
18774	S	Orysa	Y/Y	0	P	Unknown	Unknown
13656	S	Sorbi + Orysa	—	Int	SP	Unknown	Hypothetical protein
19297	S	Bradi	N/N-3′UI	NA	P	Unknown	Unknown (26)
20188	P	Frave	Y/Y	Int	P	Unknown	Unknown

Recipient column: L, Lindenbergia; P, Phelipanche; S, Striga; T, Triphysaria. Intron column: “—”, not determined; 3′UI and 5′UI mean 3′/5′-UTR introns; N/N, absence of introns in both donor and recipient; Y/Y, presence of intron in both donor and recipient gene (orthogroup 218 has two genomic transfers with introns). Expression: >2, means highly expressed in more than two stages; int, interface. D_n/D_s: P, purifying selection; POS, positive selection; RP, relaxed purifying selection; SP, stronger purifying selection. Functional category: TE, transposable element. Donor is represented by the five-letter code of species abbreviations in SI Appendix, Fig. S1. Note that the donor is the indicated taxon or an ancestor. Expression column represents the stages with primary expression for the HGT genes. Haustorial stages are 3, 4 (4.1 and 4.2), and int. For detailed information about these stages, please refer to ref. 32.