Determination of ITS1 haplotypes of Fritillariae Cirrhosae Bulbus by amplicon sequencing

Wu, Hoi-Yan; Wong, Ka-Lok; Law, Sean Tsz-Sum; Nong, Wenyang; Chan, Kwun-Tin; Hui, Jerome Ho-Lam; Lin, Ge; Chan, Wing-Han; Shaw, Pang-Chui

doi:10.1186/s13020-024-00911-3

Chinese Medicine

Table 2 Statistics of data from high throughput amplicon sequencing

From: Determination of ITS1 haplotypes of Fritillariae Cirrhosae Bulbus by amplicon sequencing

Species	Sample	Raw reads	Filtered	Denoised, merged reads	Non-chimera reads	Mapped to ITS1 of T5177 (F. unibracteata)								Identified as fungal ITS
Species	Sample	Raw reads	Filtered	Denoised, merged reads	Non-chimera reads	# Reads full-length Fritillaria ITS1	% Full-length Fritillaria ITS1	# Reads belonging to major ASVs	# Total ASVs	# Major ASVs (> 1% frequency)	% Reads w/CCCGGG	% Reads w/CTCGGG	% Reads w/CACGGG	# Fungal reads	% Fungal reads	# Fungal reads > 250 bp
F. cirrhosa	RD176-B	83,391	44,487	32,186	28,399	26,921	94.80	26,402	22	8	99.06	0.00	0.00	483	1.70	0
	RD185-B	60,733	37,116	21,945	18,085	17,445	96.46	17,169	16	10	99.35	0.24	0.00	40	0.18	36
	RD188-A	68,403	32,109	20,739	20,229	16,093	79.55	15,991	12	7	75.93	23.73	0.00	3622	17.91	49
	RD194-B	78,909	49,180	33,971	31,511	30,372	96.39	29,960	19	8	99.33	0.09	0.00	1002	3.18	0
	T4971-B	88,324	55,193	31,900	28,616	26,400	92.26	24,232	40	9	79.35	1.49	17.21	103	0.36	0
	T4972-A	80,715	48,411	25,627	24,376	22,595	92.69	20,434	53	8	90.46	1.43	2.70	249	1.02	0
	T4973-B	85,026	43,600	20,698	20,698	19,599	94.69	17,444	34	6	92.12	2.63	0.00	219	1.06	0
	T5223-A	72,061	38,426	23,249	21,082	18,497	87.74	18,206	20	7	98.91	0.39	0.00	739	3.51	12
F. delavayi	T4977-A	66,190	39,336	27,737	27,220	16,537	60.75	14,567	47	11	70.96	25.73	0.00	9567	35.15	1107
	T4978-B	220,794	133,813	94,086	76,376	61,465	80.48	56,148	91	9	78.59	19.84	0.00	8993	11.78	0
	T5234-A	69,201	41,430	26,275	23,259	20,727	89.11	19,865	27	6	55.50	42.72	0.00	1264	5.43	78
	T5235-A	78,620	44,957	32,620	26,391	22,837	86.53	22,219	22	4	98.86	0.36	0.00	124	0.47	0
	T5236-B	82,272	50,490	42,057	32,729	32,024	97.85	31,485	23	6	37.11	62.23	0.00	236	0.72	0
	T5237-B	81,155	56,949	49,840	49,804	8990	18.05	8990	4	4	91.71	8.29	0.00	27,984	56.19	12
F. przewalskii	T4979-B	94,327	62,946	39,849	32,288	30,621	94.84	29,096	38	10	83.29	14.78	0.35	111	0.34	0
	T5230-B	79,496	45,525	30,384	29,139	28,201	96.78	28,073	13	7	99.70	0.20	0.00	254	0.87	81
	T5231-B	78,000	47,880	28,276	25,094	23,051	91.86	22,686	21	11	91.59	7.48	0.00	1472	5.87	655
	T5232-B	96,145	74,152	63,946	62,846	12,574	20.01	12,461	12	8	81.54	18.36	0.00	49,779	79.21	34
	T5233-A	66,180	39,856	24,691	22,264	19,883	89.31	19,758	17	12	61.22	38.62	0.00	1893	8.50	498
F. taipaiensis	T4993-A	107,191	75,478	52,073	50,501	36,432	72.14	33,912	48	4	97.43	1.36	0.00	5761	11.41	0
	T5227-B	79,785	53,985	42,410	34,282	33,642	98.13	33,260	18	4	99.71	0.05	0.00	82	0.24	0
	T5228-A	123,092	76,756	55,043	48,937	38,073	77.80	36,783	30	5	98.28	0.38	0.00	633	1.30	0
	T5229-A	79,453	51,417	33,207	31,562	30,812	97.62	28,845	51	5	96.37	0.95	0.00	116	0.37	0
F. unibracteata	RD177-B	65,760	42,786	33,710	28,774	26,390	91.71	25,990	15	5	99.27	0.25	0.00	1047	3.64	41
	RD181-B	77,171	52,119	39,681	31,583	30,819	97.58	29,535	43	6	98.12	0.45	0.06	532	1.68	76
	T4974-A	105,170	60,311	39,083	33,381	32,489	97.33	31,005	27	6	97.34	0.35	0.00	259	0.78	0
	T4992-B	87,918	56,663	39,504	35,196	20,534	58.34	17,129	63	6	91.79	1.49	0.15	5427	15.42	0
	T5177-C	85,432	55,709	37,092	32,032	25,667	80.13	25,174	17	7	99.23	0.00	0.00	4683	14.62	0
	T5224-B	31,220	13,477	10,060	10,060	7983	79.35	6058	42	12	94.45	3.57	0.00	1726	17.16	122
F. unibracteata var. wabuensis	T4975-A	101,808	69,048	36,232	34,573	32,529	94.09	27,748	82	12	64.50	2.17	27.28	417	1.21	0
F. unibracteata var. wabuensis	T4976-B	125,753	86,110	46,991	46,603	21,894	46.98	18,303	66	15	62.67	0.00	0.00	21,613	46.38	0
F. hupehensis	RD169-B	83,488	35,812	31,038	28,181	26,132	92.73	25,204	42	3	0.00	98.69	0.00	1923	6.82	15
	RD170-A	91,109	44,873	40,561	40,287	23,831	59.15	22,582	25	3	0.48	97.72	0.00	15,707	38.99	178
	T4940-B	50,213	28,361	21,967	21,967	11,400	51.90	8747	57	29	63.81	1.90	27.77	10,126	46.10	236
	T4982-A	57,725	25,230	23,304	20,861	20,309	97.35	18,899	34	3	0.00	98.56	0.00	482	2.31	0
F. pallidiflora	RD216-B	112,772	65,531	54,317	52,481	9186	17.50	9109	11	6	8.97	89.81	0.00	43,105	82.13	0
F. pallidiflora	T5239-B	67,848	19,435	12,719	12,655	8415	66.50	8312	6	1	0.00	99.31	0.00	1556	12.30	91
F. thunbergii	T4981-A	71,190	38,222	33,819	30,877	19,170	62.09	16,933	32	4	0.00	96.80	0.00	11,623	37.64	0
F. ussuriensis	T4980-A	102,777	44,635	28,471	28,226	10,483	37.14	10,278	11	6	0.00	98.49	0.00	16,622	58.89	0
	T5221-B	57,979	36,340	33,437	33,437	0	X							32,714	97.84	0
	T5225-B	48,768	17,641	14,122	14,122	13,298	94.17	12,993	11	7	0.00	97.44	0.00	168	1.26	0
F. puqiensis	T5240-B	13,386	7338	6514	6353	0	X							899	14.15	45
F. walujewii	T4985-B	99,985	78,816	74,462	66,511	80	X							66,402	99.84	58,325

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ISSN: 1749-8546

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