Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Sep 12;8:1583.
doi: 10.3389/fpls.2017.01583. eCollection 2017.

Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships

Affiliations
Free PMC article

Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships

Xiao Zhang et al. Front Plant Sci. .
Free PMC article

Abstract

Gynostemma BL., belonging to the family Cucurbitaceae, is a genus containing 17 creeping herbaceous species mainly distributed in East Asia. It can be divided into two subgenera based on different fruit morphology. Herein, we report eight complete chloroplast genome sequences of the genus Gynostemma, which were obtained by Illumina paired-end sequencing, assembly, and annotation. The length of the eight complete cp genomes ranged from 157,576 bp (G. pentaphyllum) to 158,273 bp (G. laxiflorum). Each encoded 133 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. The four types of repeated sequences had been discovered and indicated that the repeated structure for species in the Subgen. Triostellum was greater than that for species in the Subgen. Gynostemma. The percentage of variation of the eight cp genomes in different regions were calculated, which demonstrated that the coding and inverted repeats regions were highly conserved. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Gynostemma as a member of family Cucurbitaceae. The phylogenetic relationships among the eight species were clearly resolved using the complete cp genome sequences in this study. It will also provide potential molecular markers and candidate DNA barcodes for future studies and enrich the valuable complete cp genome resources of Cucurbitaceae.

Keywords: Gynostemma BL.; characterization; chloroplast genome; comparison; phylogeny; repeats.

Figures

Figure 1
Figure 1
Gene maps of chloroplast genomes of Gynostemma BL. Genes on the inside of the large circle are transcribed clockwise and those on the outside are transcribed counterclockwise. The genes are color-coded based on their functions. Dashed area represents the GC composition of the chloroplast genome.
Figure 2
Figure 2
A radar-plot comparing features of the complete chloroplast genomes of 15 accessions of Cucurbitales species. Showing, from inside to out, overall GC content, LSC region size, number of protein-coding genes, SSC region size, IR region size, number of total genes and genome size.
Figure 3
Figure 3
The distribution, type and presence of repeated sequences and simple sequence repeats (SSR) in the cp genome of eight Gynostemma species. (A) Number of repeat sequences by length; (B) Number of three repeat types in the eight chloroplast genomes; (C) Number of SSR types in the eight chloroplast genomes; (D,E) Location of the all repeats from eight species.
Figure 4
Figure 4
Percentage of variable characters in aligned eight Gynostemma chloroplast genomes. (A) Coding region (CDS) and (B) Noncoding region (CNS); These regions are oriented according to their locations in the chloroplast genome.
Figure 5
Figure 5
Comparison of the border positions of LSC, SSC, and IR regions in four chloroplast genomes. Boxes above or below the main line represent the genes at the IR/SC borders.
Figure 6
Figure 6
Sequence identity plots among eight sequenced chloroplast genomes, with G. pentaphyllum as a reference by using mVISTA. The vertical scale indicates the identity percentage ranging from 50 to 100%. The horizontal axis corresponds to the coordinates within the chloroplast genome. Coding and non-coding regions are marked in blue and pink, respectively. Annotated genes are displayed along the top. The black boxes show the two IR regions.
Figure 7
Figure 7
Phylogenetic relationship of the 17 species inferred from BI and ML analyses based on the complete cp genome sequences. The Bayesian posterior probabilities and bootstrap values of ML analyses are shown beside the clades. Castanea mollissima and Castanea pumila var. pumila were used as the outgroups.

Similar articles

See all similar articles

Cited by 10 articles

See all "Cited by" articles

References

    1. Asif H., Khan A., Iqbal A., Khan I. A., Heinze B., Azim M. K. (2013). The chloroplast genome sequence of Syzygium cumini (L.) and its relationship with other angiosperms. Tree Genet. Genomes 9, 867–877. 10.1007/s11295-013-0604-1 - DOI
    1. Balakirev E. S., Ayala F. J. (2003). Pseudogenes: are they junk or functional DNA? Annu. Rev. Genet. 37, 123–151. 10.1146/annurev.genet.37.040103.103949 - DOI - PubMed
    1. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., et al. . (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477. 10.1089/cmb.2012.0021 - DOI - PMC - PubMed
    1. Bock D. G., Kane N. C., Ebert D. P., Rieseberg L. H. (2014). Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke. New Phytol. 201, 1021–1030. 10.1111/nph.12560 - DOI - PubMed
    1. Boetzer M., Pirovano W. (2012). Toward almost closed genomes with GapFiller. Genome Biol. 13:R56. 10.1186/gb-2012-13-6-r56 - DOI - PMC - PubMed

LinkOut - more resources

Feedback