Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes

Abstract Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old New Worlds, except Europe. The relationships among this family have been suggested several morphological molecular studies. However, it is difficult to explain their due high variations low support values. Currently, many researchers using complete chloroplast genome data for inferring evolution of land plants. In study, we completed 15 new plastid sequences subfamily Commelinoideae Mi-seq platform. We utilized reveal structural reconstruct problematic positions first time. Results All examined species three pseudogenes ( acc D, rpo A, ycf 15), former two might be a synapomorphy within Commelinales. Only four tribe Commelineae presented IR expansion, which affected duplication rpl 22 gene. identified inversions that range from approximately 3 kb taxa Amischotolype , Belosynapsis Murdannia Streptolirion ). phylogenetic analysis 77 protein-coding genes with maximum parsimony, likelihood, Bayesian inference suggests Palisota most closely related Commelineae, supported by This result differs significantly current classification Commelinaceae. Also, resolved unclear position Streptoliriinae monophyly Dichorisandrinae. Among ten CDS ndh H, C2, rps 3, G, ccs F, mat K, 1), nucleotide diversity values (Pi > 0.045) over 500 bp length, 1) show they congruent topology derived genes. Conclusions provide detailed information on genomes taxa. characteristic diversity, can used infer evolutionary history. further research needed revise