Evaluation of DNA barcoding efficiency of cpDNA barcodes in selected Philippine Leea L. (Vitaceae)

Figures & data

Table 1. List of Leea species collected in different Philippine provinces showing USTH voucher numbers.

Taxa	Code	Location	USTH number
L. aculeata	13912, 14A026	Quezon, Surigao del Sur	012443, 012016
L. congesta	121007, 13028	Samar, Ilocos	011231, 011232
L. guineensis	12080, 12A018, 12501	Mindoro, Bicol, Surigao del Sur	011243, 011228, 011246
L. philippinensis	12563	Surigao del Sur	011255

Figure 1. Field photographs of Leea species. (A) Habit and (B) infructescence of Leea aculeata. (C) Habit and (D) close-up of inflorescence of Leea guineensis.

Table 2. Universal primers of the four candidate barcodes used in the study.

Candidate barcode	Primer pair	Sequence (5' → 3')
matK	3F_Kim f	CGTACAGTACTTTTGTGTTTACGAG
	1R_Kim r	ACCCAGTCCATCTGGAAATCTTGGTTC
rbcL	rbcL_aF	ATGTCACCACAAACAGAGACTAAAGC
	rbcL_aR	CTTCTGCTACAAATAAGAATCGATCTC
trnH-psbA	trnHf_05	CGCGCATGGTGGATTCACAATCC
	psbA3'f	GTTATGCATGAACGTAATGCTC
trnL-F	c	CGAAATCGGTAGACGCTACG
	f	ATTTGAACTGGTGACACGAG

Table 3. Sequence characteristics from multiple sequence alignment of the four candidate barcodes used in this study.

Parameter	Candidate barcode
	matK	rbcL	trnH-psbA	trnL-F
Aligned length (bp)	847	547	592	927
Mean length (bp)	788.5	530.2	513.9	893.9
Variable sites (bp)	13	15	72	240
Parsimony informative (bp)	9	9	37	31

bp, base pairs.

Figure 2. Efficiency of polymerase chain reaction amplification and sequencing success rates of the four candidate barcodes for the selected Leea sp.

Table 4. Calculated mean interspecific and intraspecific divergences of the four candidate barcodes using Kimura two-parameter.

Parameter	Candidate barcode
	matK	rbcL	trnH-psbA	trnL-F
Mean interspecific	0.007±0.003	0.009±0.010	0.052±0.030	0.055±0.071
Mean intraspecific	0.000±0.001	0.006±0.005	0.021±0.014	0.032±0.607

Figure 3. Neighbour-joining tree of (A) matK, (B) rbcL, (C) trnH-psbA and (D) trnL-F sequences inferred using Kimura two-parameter distances.

Table 5. Wilcoxon two-sample test for interspecific and intraspecific divergences of the four candidate barcodes.

Parameter	Candidate barcode
	matK	rbcL	trnH-psbA	trnL-F
Number of interspecific	37	37	54	78
Number of intraspecific	8	8	12	13
Wilcoxon W	45	134.5	231	386.5
p value	3.931 × 10^–5	0.1458	0.004589	0.01671

Table

Taxa	Candidate barcode
	GenBank Accession No.		EMBL Accession No.
	matK	rbcL	trnH-psbA	trnL-F
L. aculeata	KT735195KT735196	KT735197KT735199	LN883861LN883862	LN883857
L. congesta	KT735193KT735194	KT735200	LN883863	LN883856
L. guineensis	KT735189KT735190KT735191	KT735201KT735202KT735203	LN883858LN883859LN883860	LN883852LN883853LN883854
L. philippinensis	KT735192	KT735198	LN883864	LN883855