Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification

Table 3 Efficiency of PCR and sequence characterization of DNA barcodes

DNA barcodes	No. of sequences	PCR success rates (%)	Aligned length (bp)	Number	Variable sites	K2P	Species identification success rates ^a (%)
DNA barcodes	No. of sequences	PCR success rates (%)	Aligned length (bp)	Number	Number (%)	K2P	Species identification success rates ^a (%)
ITS2	36	97.30	236	87	36.86	0.000-0.411	76.92%
ITS	36	97.30	682	174	25.51	0.000-0.046	38.46%
matK	10	27.03	725	429	59.17	0.000-1.168	15.38%
rbcL	29	78.38	657	15	2.28	0.000-0.018	23.08%
psbA-trnH	33	89.19	797	469	58.85	0.000-1.124	23.08%
ndhB_rps7	37	100	297	2	6.73	0.000-0.004	0
psaI_ycf4	37	100	342	12	3.51	0.000-0.018	23.08%
trnC-GCA_petN	37	100	507	251	49.51	0.000-0.768	30.77%
rpl20	36	97.30	297	21	7.07	0.000-0.026	30.77%
rpl33	36	97.30	148	5	3.38	0.000-0.035	0
ccsA	34	91.89	939	33	3.51	0.000-0.023	38.46%
rps3	34	91.89	589	83	14.09	0.000-0.090	30.77%
rpoA	33	89.19	907	62	6.84	0.000-0.021	30.77%
rps4	36	97.30	599	40	6.68	0.000-0.025	23.08%
ndhD_1	35	94.59	681	18	2.64	0.000-0.020	15.38%
ndhD_2	34	91.89	645	44	6.82	0.000-0.025	23.08%

^a When the accessions of one species were clustered in one clade in the ML tree, it was considered successfully identified. Species identification success rates were the number of successfully identified species divided by the total number of detected species (13)

ISSN: 1471-2229