Supplementary Material: Table 1 Primers and pcr conditions used in this study

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Supplementary Material:

Table 1 Primers and PCR conditions used in this study

Target	Primer	Primer Sequence (5’  3’)	PCR Product (bp)	Altered reaction conditions	Altered thermocycling conditions	Reference
Bacterial 16S rRNA gene	27F	agagtttgatcctggctcag	1400
	1494R	ggttaccttgttacgactt
Fungal 18S rRNA gene	nu-ssu-0817	ttagcatggaatrrattagga	719		35 cycles: 94°C for 30 s, 56°C for 10 s, 72°C for 30 s
	nu-ssu-1536	attgcaatgcyctatcccca
Adenylation domain bacterial NRPSs	MTF2	gcnggyggygcntaygtncc	~1000		94°C for 10 s, 55°C for 30 s, 72°C for 1 min
	MTR2	ccncgdatyttnacytg
Ketosynthase domain of bacterial PKSs	DKF	gtgccggtnccrtgngyytc	~650-700		94°C for 10 s, 52°C for 30 s, 72°C for 1 min
	DKR	gcgatggayccncarcarmg
Adenylation domain of fungal NRPSs	RJ016-R	arrtcnccngtyttrta	~300		94°C for 30 s, 50°C for 30 s, 60°C for 1 min; final extension: 60°C for 1 min
	RJ016-F	tayggnccnacnga
Ketosynthase domain of fungal PKSs	LC1	gayccimgittyttyaayatg	~700	Primers (pmol): LC1, 50; LC2c, 8; LC3, 24; LC5c, 16	94°C for 30 s, 56°C for 10 s, 72°C for 30 s
	LC2c	gticcigticcrtgcatytc
	LC3	gcigarcaratggayccica	~700
	LC5c	gtigaigticrtgigcytc

Table 2 BLASTN analysis of 16S rRNA gene sequences of bacterial endophytes

Isolate	Closest BLAST Similarity	Accession Number ^a	Identity (%)	Coverage (%)
Bletilla striata
B1	Bacillus cereus	FJ908707	100	100
B2	Bacillus cereus	FJ908707	100	100
B3	Paenibacillus sp.	FJ174615	99	100
B4	Paenibacillus sp.	FJ174615	99	100
B5	Bacillus cereus	FJ908707	100	100
B6	Bacillus cereus	FJ908707	100	100
B7	Bacillus cereus	FJ908707	100	100
B8	Bacillus cereus	FJ908707	100	100
B9	Enterobacter sp.	AM396909	98	100
B10	Enterobacter sp.	AM396909	98	100
B11	Bacillus cereus	FJ908707	100	100
B12	Bacillus cereus	FJ908707	100	100
B13	Bacillus cereus	FJ908707	100	100
B14	Paenibacillus barcinonensis	FJ174615	99	100
B15	Paenibacillus barcinonensis	FJ174615	99	100
B16	Enterobacter sp.	AM396909	99	100
B17	Enterobacter sp.	AM396909	99	100
B18	Bacillus cereus	FJ581461	99	100
Lycium chinense
B19	Enterobacter ludwigii	EF175735	98	99
B20	Bacillus thuringiensis	FJ544327	100	100
B21	Staphylococcus epidermidis	FJ217188	99	100
B22	Pseudomonas lurida	AJ581999	99	100
B23	Pseudomonas sp.	FJ225205	99	100
B24	Pseudomonas lurida	AJ581999	99	100
B25	Pseudomonas sp.	FJ225205	99	100
B26	Pseudomonas sp.	FJ225205	99	100
B27	Pseudomonas poae	FJ179369	99	100
B28	Bacillus thuringiensis	EU429664	100	99
B29	Bacillus thuringiensis	EU429664	100	100
Pinellia ternata
B30	Paenibacillus barcinonensis	FJ174615	99	100
B31	Paenibacillus barcinonensis	FJ174615	99	100
B32	Paenibacillus barcinonensis	FJ174615	99	100
B33	Paenibacillus barcinonensis	FJ174615	99	100
B34	Paenibacillus barcinonensis	FJ174615	99	100
B35	Paenibacillus barcinonensis	FJ174615	99	100
B36	Paenibacillus barcinonensis	FJ174615	99	100
B37	Paenibacillus barcinonensis	FJ174615	99	100
Leonurus heterophyllus
B42	Pseudomonas sp.	FJ436428	100	100
B43	Pseudomonas sp.	FJ436428	100	100
B44	Pseudomonas sp.	FJ436428	100	100
B45	Pseudomonas sp.	FJ436428	100	100
B47	Staphylococcus pasteuri	FJ380982	100	100
B49	Bacillus cereus	AE016877	100	100
B50	Bacillus sp.	FJ528077	100	100
B51	Bacillus cereus	EU429664	100	100
Digitalis purpurae
B52	Enterobacteriaceae bacterium	EU029105	100	100
B53	Bacillus cereus	CP000227	100	100
B54	Enterobacteriaceae bacterium	EU029105	100	100
B55.1	Bacillus cereus	CP000227	100	100
B55.2	Enterobacteriaceae bacterium	EU029105	100	100
B56	Swine manure bacterium	AY167970	100	99
F_21	Methylobacterium sp.	FJ267582	100	100
Belacamda chinense
B58.2	Klebsiella pneumoniae	CP000964	100	100
B59	Bacillus cereus	CP000227	100	100
B60	Klebsiella pneumoniae	CP000964	100	100
B61	Bacillus sp.	FJ561297	100	100
B62	Moraxella sp.	EU260324	100	100
B63	Bacillus sp.	FJ561297	100	100
B64	Paracoccus sp.	AM989037	100	100
B65.1	Bacillus safensis	FJ577677	99	100
B65.2	Microbacterium sp.	EU181227	100	100
B67	Bacillus subtilis	FJ460478	99	100
B68	Bacillus flexus	FJ22676	99	100
F22	Achromobacter xylosoxidan	EU373389	100	100
F23	Sphingomonas sp.	AB076396	98	99
F25	Sphingomonas sp.	AB076396	98	99
F29	Sphingomonas rosa	D13945	97	100
F33	Sphingomonas rosa	D13945	98	100
F35	Sphingomonas rosa	D13945	99	100
F36	Sphingomonas rosa	D13945	98	100
F37	Sphingomonas rosa	D13945	98	100
Pinellia pedatisecta
F11	Citrobacter freundii	EU980035	99	100
F12	Endophytic bacterium	FJ205675	100	100
F13	Enterobacter sp.	FJ587226	100	100

^aClosest related species in the NCBI sequence database. When two or more sequences were equally similar, only the first sequence is given.

Table 3 BLASTN analysis of 18S rRNA gene sequences of fungal endophytes

Isolate	Closest Match ^a	Accession number	Identity (%)	Coverage (%)
P. ternata
F1	Cladosporium sp.	EF392680	100	100
F2	Cochliobolus sativus	DQ677995	100	100
F3	Lasiobolidium spirale	DQ646533	100	100
F4	Cladosporium sp.	EF392680	100	100
L. chinense
F5	Cladosporium cladosporioides	EU263604	100	100
F6	Fusarium sp.	FJ216403	100	100
F18	Davidiella macrospora	EU167591	100	100
B. striata
F8	Ascomycota sp.	EU887770	99	100
P. pedatisecta
F9	Dendryphion nanum	AY382475	100	100
F10	Cordyceps gunnii	DQ838790	100	100
F14	Dendryphion nanum	AY382475	100	100
F15	Dendryphion nanum	AY382475	100	100
F19	Fusarium sp.	FJ216403	99	100
D. purpurae
F16	Mycosphaerella podagrariae	EU386700	100	100
F17	Mycosphaerella podagrariae	EU386700	100	100
F24	Fusarium sp.	EU710826	100	100
F28	Guignardia mangiferae	AB041249	100	100
T. yunnanensis
F38	Alternaria sp	FJ515320	100	100
F39	Fusarium sp.	EU710826	100	100
F40	Phoma sp.	FJ515319	100	100
F41	Phoma sp.	FJ515319	100	100
F42	Phoma sp.	FJ515319	100	100
F43	Phoma sp.	FJ515319	100	100
F44	Phoma sp.	FJ515319	100	100
F45	Phoma sp.	FJ515319	100	100
F46	Colletotrichum sp.	AB076801	100	100
F48	Pestalotiopsis guepinii	EU375526	100	100
F49	Pestalotiopsis guepinii	EU375526	100	100
F50	Pestalotiopsis guepinii	EU375526	100	100
F51	Phomopsis sp.	AY190250	100	100
F52	Davidiella tassiana	EU167558	99	100
F53	Ascomycota sp.	DQ381536	97	100
F54	Pestalotiopsis guepinii	EU375526	100	100
F55	Pestalotiopsis guepinii	EU375526	100	100
F56	Pestalotiopsis guepinii	EU375526	100	100
F58	Colletotrichum sp.	AB076801	99	100

^aClosest related species in the 18S rRNA gene sequence database. When two or more sequences were equally similar, only the first sequence is given.

Fig. 1 Multiple sequence alignment of the active region of KS domain fragments amplified from bacteria and fungi. The residues encompassing the cysteine active site are indicated by a surrounding box.