Comparative Analysis of Cichorieae Tribe (Asteraceae) Chloroplast Genomes: Insight to Structure, Repetitive DNA, and Phylogeny.

The whole chloroplast genome has been increasingly used over the past three decades for systematic and ordered analysis of evolutionary relationships, variation within species, and developmental studies. There were several other studies on the Asteraceae family, but the studies were on the family level. This study investigates the plastomes of an important Asteraceae tribe, Cichorieae, that are widely distributed, morphologically complex, include several species reproduce apomictically. Plastomes belonging to 36 different species in 12 different genera have been studied in detail and compared. The comparisons were based on plastome structure, number of coding and noncoding genes, and number of rRNA and tRNA genes. Further, the repetitive DNA types, frequency, and their position in the chloroplast genomes have been analyzed. Moreover, SSRs types and frequency were compared and analyzed. In addition, a number of coding and noncoding regions were studied and used to construct a phylogenetic tree. The investigation of this study indicated the distinctiveness of sequence divergence among the plastomes of Cichorieae tribe species in various aspects. The results provided excellent phylogenetic linkages that can be used for advanced comparative studies at both generic and species levels. Most noncoding and coding regions showed the least variation; however, major variations were shown by those regions that have rarely been used in chloroplast phylogenetics. Regions of coding (clpP, matK, ndhA, rpoC1, rpoC2, and ycf1) and non-coding (ndhF-rpl32, petN-psbM, psbE-petL, rps4-ndhJ, rps15-ycf1, trnLtrnF, trnT-psbD, and ycf3-trnS) are recommended to use in studying Cichorieae tribe members to achieve better phylogenetic construction, population genetic analysis, and use as a marker for accurate and automated species identification. The tandem repeat of 21-30 period size is the most variable among the Cichorieae tribe plastomes. Ttra-, penta-, and hexanucleotide SSR types were found in Cichorium intybus, Crepidiastrum, Sonchus, and Taraxacum plastomes, while, they were not found in other plastomes under study. These SSRs may be useful for identifying species, detecting hybridization, determining phylogeny, and differentiating populations. [ABSTRACT FROM AUTHOR]