The complete chloroplast genome sequence of Gynostemma yixingense and comparative analysis with congeneric species

Abstract

Gynostemma yixingense, an important medicinal member of the Cucurbitaceae family, is an endemic herbaceous species distributed in East China. It is morphologically similar to the plants in the same genus, which resulted in some confusion in identification and application. Meanwhile, there are still some controversies in taxonomy. Herein, the complete chloroplast genome sequence of G. yixingense was obtained by Illumina paired-end sequencing technology and compared to other chloroplast genome sequences of congeneric species. The complete chloroplast genome of G. yixingense is 157,910 bp in length with 36.94% GC content and contains a large single-copy (LSC) region of 86,791 bp, a small single-copy (SSC) region of 18,635 bp and a pair of inverted repeat (IR) regions of 26,242 bp. The whole genome contains 133 unique genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. In addition, 74 simple sequence repeats (SSRs) were identified, most of which were A/T rich. The phylogenetic analysis indicated that G. yixingense had the closest relationship to G. laxiflorum. The result of this study provided an important theoretical basis for chloroplast genome and phylogenetic analysis of G. yixingense.

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

“…Furthermore, we downloaded all the available chloroplast genomes for this genus and performed a comprehensive analysis of the chloroplast genomes of this basal group of Cucurbitaceae. The chloroplast genomes of different species of Gynostemma are highly conserved, and the gene compositions, structures and GC contents are similar, RNA editing sites and condon usage bias showing close species relationships within the genus Gynostemma [ 13 , 17 , 18 , 19 , 20 , 21 , 51 ]. Our newly sequenced chloroplast genomes of Gynostemma species revealed differences between the two subgenera, despite the low chloroplast polymorphism in this genus.…”

“…These advantages of chloroplast genomes make them an ideal tool for phylogenetic and taxonomic studies [ 16 ]. There have been multiple separate reports involving the complete chloroplast genome of a single Gynostemma species [ 17 , 18 , 19 , 20 ]. The chloroplast genomes of eight species from the Gynostemma genus were sequenced in Zhang’s study [ 21 ].…”