Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2

Table 1

Intragenomic diversity analysis of ITS2 major variants from the 18 Dendrobium species.

Taxon	Number of total 454 sequences	Number of total variants	Variant name (>1% emergence frequency)	Percentage of each variant (>1%)	Length (bp)	G + C content (%)	Intragenomic sequence distances (>1% emergence frequency)
D. crepidatum	1919	4	p1-1	99.27	248	50.81	0
D. aphyllum	1888	19	p2-1	95.87	248	52.42	0
D. devonianum	722	8	p3-1	95.43	248	49.20	0.004
			p3-2	1.80	247	48.58
D. officinale	2554	10	p4-1	93.89	246	50.81	0
			p4-2	4.78	245	51.02
D. denneanum	1270	15	p5-1	91.50	248	51.21	0.016
			p5-2	2.36	248	50.81
			p5-3	1.42	248	50.00
			p5-4	1.18	248	50.81
D. nobile	578	7	p6-1	63.15	246	53.66	0.017
			p6-2	14.36	246	54.07
			p6-3	10.73	246	54.07
			p6-4	9.69	246	52.85
D. chrysanthum	860	30	p7-1	76.74	245	52.24	0.051
			p7-2	3.14	245	51.84
			p7-3	3.02	244	52.05
			p7-4	2.56	245	47.35
			p7-5	1.74	245	48.16
			p7-6	1.63	245	47.76
			p7-7	1.28	245	48.57
			p7-8	1.28	245	50.20
			p7-9	1.28	244	52.46
D. primulinum	3690	36	p8-1	75.93	248	53.63	0.005
			p8-2	9.51	248	53.23
			p8-3	9.11	248	53.23
D. chrysotoxum	2366	55	p9-1	63.82	249	55.42	0.081
			p9-2	19.95	249	55.82
			p9-3	2.79	249	55.02
			p9-4	2.20	247	52.63
			p9-5	2.20	249	55.42
			p9-6	1.65	247	53.04
D. loddigesii	1593	47	p10-1	39.55	248	52.02	0.009
			p10-2	30.70	248	51.21
			p10-3	14.44	248	52.42
			p10-4	5.34	248	51.21
D. acinaciforme	1112	30	p11-1	70.05	248	52.42	0.045
			p11-2	16.55	248	52.42
			p11-3	6.56	248	53.23
D. williamsonii	182	52	p12-1	25.82	247	52.63	0.05
			p12-2	3.85	247	52.23
			p12-3	2.75	247	50.20
			p12-4	3.75	247	51.01
			p12-5	2.20	247	51.01
			p12-6	2.20	247	51.82
			p12-7	2.20	247	50.20
			p12-8	2.20	247	48.99
			p12-9	2.20	247	50.61
			p12-10~p12-21	19.80	247–250	48.99–51.42
			p12-22~p12-52	34.10	244–247	48.37–52.63
D. capillipes	1610	33	p13-1	93.03	251	50.20	0.004
			p13-2	1.43	251	49.80
D. crystallinum	1197	14	p14-1	51.96	250	55.60	0.005
			p14-2	39.52	250	55.60
			p14-3	5.93	250	55.20
D. gratiosissimum	1167	8	p15-1	93.23	246	52.85	0.004
			p15-2	5.14	246	52.44
D. trigonopus	1906	27	p16-1	93.34	251	51.00	0
D. wardianum	2778	21	p17-1	84.38	250	56.00	0
			p17-2	12.35	251	55.78
D. pendulum	2232	19	p18-1	49.73	250	54.00	0.005
			p18-2	24.82	250	53.20
			p18-3	20.79	249	53.41
			p18-4	1.43	250	53.60
			p18-5	1.25	250	53.60

variations were caused by insert/deletion, which was treated as complete deletion when calculating the K2P distances. Thus, the K2P distances turned out to be zero.