Abstract
BackgroundCommelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in 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. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time.ResultsAll examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes.ConclusionsIn this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.
Highlights
Commelinaceae Mirb., commonly known as the dayflower and spiderwort family, are the largest family of Commelinales Mirb. ex Bercht. & J
Chloroplast genome assembly and annotation We completed 15 new plastid genomes in this study listed in Table 1 through 9 to 21 million raw reads for each species (Fig. S1, Table S1)
Compared with other Commelinales, we found two characteristic pseudogenes in all members of Commelinoideae, which might be a synapomorphy within the order
Summary
Commelinaceae Mirb., commonly known as the dayflower and spiderwort family, are the largest family of Commelinales Mirb. ex Bercht. & J. Commelinaceae Mirb., commonly known as the dayflower and spiderwort family, are the largest family of Commelinales Mirb. Commelinaceae consist of 41 genera and approximately 730 species, widely distributed in both the Old and New Worlds, except in Europe [2,3,4]. The flowering unit (inflorescence) of Commelinaceae is a manybranched thyrse, with each branch generally consisting of a many-flowered cincinnus. Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. We completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time
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