Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes

Background: Commelinaceae (Commelinales) comprise 41 genera and widely distributed in both the Old and New Worlds except Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Nowadays, many researchers are commonly using complete chloroplast genome data for inferring evolution of land plants. In this study, we completed 15 new chloroplast genome sequences of subfamily Commelinoideae using Mi-seq platform. We utilized genome data for the first time to reveal the structural variations and reconstruct the problematic positions of genera. Results: All examined species of Commelinoideae have three pseudogenes ( acc D, rpo A, and ycf 15) and former two genes might be a synapomorphy within the Commelinales. Only four species in tribe Commelineae appear IR expansion which affected duplication of rpl 22 gene. We identified inversions which range from approximately 3 to 15 kb from four taxa ( Murdannia , Streptolirion , Amischotolype , and Belosynapsis ). The phylogenetic analyse using 77 chloroplast protein coding genes with maximum parsimony, maximum likelihood, and the Bayesian inference suggest that Palisota connected with tribe Commelineae with high support values, differ from recent classification of Commelinaceae. Also, we resolved unclear position of Streptoliriinae and monophyly of Dichorisandrinae. Conclusions: In this study, we provide detailed information of the 15 plastid genomes of Commelinaceae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used for inferring evolutionary history about this family. Also, we need a further research to revise position of Palisota in recent classification.