The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus

Abstract

Gynostemma is an important medicinal and food plant of the Cucurbitaceae family. The phylogenetic position of the genus Gynostemma in the Cucurbitaceae family has been determined by morphology and phylogenetics, but the evolutionary relationships within the genus Gynostemma remain to be explored. The chloroplast genomes of seven species of the genus Gynostemma were sequenced and annotated, of which the genomes of Gynostemma simplicifolium, Gynostemma guangxiense and Gynostemma laxum were sequenced and annotated for the first time. The chloroplast genomes ranged from 157,419 bp (Gynostemma compressum) to 157,840 bp (G. simplicifolium) in length, including 133 identical genes: 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. Phylogenetic analysis showed that the genus Gynostemma is divided into three primary taxonomic clusters, which differs from the traditional morphological classification of the genus Gynostemma into the subgenus Gynostemma and Trirostellum. The highly variable regions of atpH-atpL, rpl32-trnL, and ccsA-ndhD, the repeat unilts of AAG/CTT and ATC/ATG in simple sequence repeats (SSRs) and the length of overlapping regions between rps19 and inverted repeats(IRb) and between ycf1 and small single-copy (SSC) were found to be consistent with the phylogeny. Observations of fruit morphology of the genus Gynostemma revealed that transitional state species have independent morphological characteristics, such as oblate fruit and inferior ovaries. In conclusion, both molecular and morphological results showed consistency with those of phylogenetic analysis.

Complete Chloroplast Genome Sequences of Two Ehretia Trees (Ehretia cymosa and Ehretia obtusifolia): Genome Structures and Phylogenetic Analysis

“…The arrangement and recombination of the cp genome may be significantly influenced by the regions and the numbers of the repeat sequences [61]. The long repeat sequence analysis revealed that palindromic and forward repeats were the most common repeats in E. cymosa and E. obtusifolia (Figure 5), which is consistent with other angiosperm cp genome analyses [62][63][64][65][66]. The SSRs analysis showed that the cp genomes of E. cymosa and E. obtusifolia comprised 141 SSRs and 139 SSRs, respectively (Table 2).…”

Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

“…The number and regions of repeat sequences might be the reason for the recombination and arrangement events in the chloroplast genome [71]. The palindromic and forward repeats are the dominant types of repeats in the angiosperm plastomes [72][73][74]. The SSRs analysis revealed that both genomes contained 155 microsatellites (Table 2).…”