Table 1 Gene clusters inferred by different tree inference methods (Maximum Likelihood and Bayesian Inference) and lists of genes in each cluster. Bolded gene names depict distinct genes revealed by two methods in each cluster. Note that the ycf1 gene is clustered with the combined tree dataset based on the Maximum Likelihood method, thus is not listed here

Cluster 1

(8 shared)

8 genes: chlB, matK, ndhA, ndhF, ndhH, rpoC2, rps2, ycf2

14 genes: atpF, chlB, matK, ndhA, ndhF, ndhH, psbK, rpl2, rpoA, rpoB, rpoC2, rps2, ycf1, ycf2

Cluster 2

(56 shared)

62 genes: accD, atpA, atpB, atpF, atpH, atpI, ccsA, cemA, chlL, chlN, clpP, infA, ndhB, ndhC, ndhD, ndhG, ndhI, ndhJ, ndhK, petA, petB, petD, petL, petN, psaA, psaB, psbA, psbB, psbC, psbD, psbE, psbH, psbI, psbK, psbL, psbN, psbZ, rbcL, rpl2, rpl14, rpl16, rpl20, rpl22, rpl23, rpl32, rpl36, rpoA, rpoB, rpoC1, rps12, rps14, rps15, rps16, rps18, rps19, rps3, rps4, rps7, rps8, ycf12, ycf3, ycf4

56 genes: accD, atpA, atpB, atpH, atpI, ccsA, cemA, chlL, chlN, clpP, infA, ndhB, ndhC, ndhD, ndhG, ndhI, ndhJ, ndhK, petA, petB, petD, petL, petN, psaA, psaB, psbA, psbB, psbC, psbD, psbE, psbH, psbI, psbL, psbZ, rbcL, rpl14, rpl16, rpl20, rpl22, rpl23, rpl32, rpl36, rpoC1, rps12, rps14, rps15, rps16, rps18, rps19, rps3, rps4, rps7, rps8, ycf12, ycf3, ycf4

Cluster 3

(11 shared)

11 genes: atpE, ndhE, petG, psaC, psaI, psaJ, psbF, psbJ, psbM, psbT, rps11

12 genes: atpE, ndhE, petG, psaC, psaI, psaJ, psbF, psbJ, psbM, psbN, psbT, rps11