Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

Table 3 Evolutionary characteristics of 17 highly diverged protein-coding genes in the Artemisia plastome

Gene^a	Length of alignment (bp)	Avg. pairwise similarity (%)^b	Identical sites (%)	π	H	Total variable sites	Singleton sites	PI sites	Ka/Ks^c
ycf1	5076	98.96	94.2	0.0065	24	44	21	23	0.6674
accD	1572	98.7	92.8	0.0057	19	42	12	30	1.0568
infA	231	99.63	97.9	0.0037	7	5	2	3	0.0097
ndhE	303	99.63	98.4	0.0036	6	5	2	3	0.0295
rps8	402	99.67	98.5	0.0033	7	6	1	5	0.3830
ndhF	2223	99.7	98.5	0.0030	18	32	9	23	0.1783
psaC	243	99.71	98.4	0.0029	5	4	2	2	0
petD	480	99.71	98.3	0.0029	8	8	4	4	0.0112
rpl22	471	99.66	97.3	0.0027	9	7	3	4	0.1161
psbT	99	99.76	97.1	0.0025	4	3	3	0	0
rpl16	405	99.73	98.8	0.0022	6	5	1	4	0
rpl36	111	99.8	98.2	0.0020	2	2	0	2	0
matK	1515	99.52	97.6	0.0019	16	20	11	9	0.2803
rps3	654	99.69	98.3	0.0018	12	11	4	7	0.1808
psbK	177	99.67	98.9	0.0017	3	2	1	1	0.1924
rpoC2	4137	99.8	98.5	0.0017	22	56	36	20	0.3194
petB	645	99.78	98.8	0.0016	9	8	4	4	0
Overall	68,214	99.50	98.2	0.0015	28	769	402	367	0.1774

^aGenes with > 0.2% average pairwise dissimilarity and > 0.0015 π values were selected
^bCoding sequences were aligned using MUSCLE and translational alignment in Geneious Prime
^cKa/Ks values (ω) were calculated according to Yang and Nielsen (2000) [43] using the yn00 program in the PAML 4 package

ISSN: 1471-2164