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

Abstract

BackgroundCommelinaceae (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 (accD, rpoA, and ycf15) and former two genes might be a synapomorphy within the Commelinales. Only four species in tribe Commelineae appear IR expansion which affected duplication of rpl22 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.

Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

“…In the Eriocaulon chloroplast genomes, we found 33 to 58 SSR loci. Other studies have shown that the most abundant SSRs were A/T-rich mononucleotide repeats, which was consistent with the chloroplast genome's common polyA or polyT repeats and rare G or C repeats [35,[51][52][53]. Dinucleotide repeats were the most common type in the Eriocaulon chloroplast genomes (Table 2) and had high AT content.…”

Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

“…In most plants, the IRb and SSC boundary lie on the ycf1 gene, which may be associated with the expansion of the IRb/SSC boundary (Kumar et al, 2018). In the cp genome of A. ukurunduense, we also observed the ycf15 gene, which exists in most angiosperms but whose function remains unknown (Shi et al, 2013;Jung et al, 2021). Compared with the LSC and SSC regions, GC content in the IR region was the highest, mainly due to four rRNA genes occupying a greater area.…”