Table 1. Dcl, Rdr, Ago and MIRNA genes in three Phytophthora species.

Group	Locus	Locus accession	Position
Rdr1	PiRdr1	PITG_10457	Supercontig 18∶1359241–1367325+
Rdr1	PsRdr1	estExt_Genewise1Plus.C_3_t40457	Scaffold 3∶2028009–2036275+
Rdr1	PrRdr1	N/A1	Scaffold 67∶79140–87321−
Dcl1	PiDcl1	PITG_09292	Supercontig 14∶1931317–1936311+
Dcl1	PsDcl1	gm1.19145_g	Scaffold 10∶1947580–1952607−
Dcl1	PrDcl1	C_scaffold_46000013	Scaffold 46∶152941–157809−
Dcl2	PiDcl2	N/A1	N/A1
Dcl2	PsDcl2	fgenesh1_pg.4_#_534	Scaffold 4∶2583558–2586463−
Dcl2	PrDcl2	fgenesh1_pg.C_scaffold_43000060	Scaffold 43∶164754–168440−
Ago1	PiAgo1	PITG_04470	Supercontig 5∶4373459–4376242−
Ago1	PiAgo22	PITG_04471	Supercontig 5∶4396571–4399354−
Ago1	PsAgo1	Physo2.s_453613	Scaffold 11∶289545–292340−
Ago1	PrAgo1	C_scaffold_37000014	Scaffold 37∶196057–199708+
Ago3	PiAgo3	PITG_01400	Supercontig 2∶1325116–1328925−
Ago3	PsAgo3	fgenesh1_pg.4_#_308	Scaffold 4∶1735957–1739823+
Ago3	PrAgo3	N/A1	Scaffold 18∶380881–384807−
Ago4	PiAgo4	PITG_01443	Supercontig 2∶1512873–1515521−
Ago4	PsAgo4	e_gw1.4.3046.1	Scaffold 4∶1590683–1593337−
Ago4	PrAgo4	fgenesh1_pg.C_scaffold_18000159	Scaffold 18∶445984–449397−
Ago5	PiAgo5	PITG_01444	Supercontig 2∶1518134–1520629−
Ago5	PsAgo5	fgenesh1_pm.4_#_266	Scaffold 4∶1586191–1588686−
Ago5	PrAgo5	C_scaffold_18000063	Scaffold 18∶453298–459311+
Ago6	PsAgo6	fgenesh1_pg.4_#_282	Scaffold 4∶1601071–1603176−
Ago7	PrAgo7	N/A1	Scaffold 104∶81401–85778+
MIR8788	pin-MIR8788	N/A1	Supercontig 18∶1064102–1064237−
MIR8788	psj-MIR8788a	N/A1	Scaffold 3∶1772538–1772675−
MIR8788	psj-MIR8788b	N/A1	Scaffold 3∶1777195–1777334+
MIR8788	pra-MIR8788a	N/A1	Scaffold 67∶213512–213649−
MIR8788	pra-MIR8788b	N/A1	Scaffold 1330∶2306–2443+

¹See File S2 for sequences.

² PiAgo1 and PiAgo2 are co-orthologs with PsAgo1 and PrAgo1, therefore, the name Ago2 was not assigned to any gene in P. sojae or P. ramorum.