Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species

Abstract

The complete plastome sequences of six species were sequenced to better understand the evolutionary relationships and mutation patterns in the chloroplast genome of the genus Colobanthus. The length of the chloroplast genome sequences of C. acicularis, C. affinis, C. lycopodioides, C. nivicola, C. pulvinatus and C. subulatus ranged from 151,050 to 151,462 bp. The quadripartite circular structure of these genome sequences has the same overall organization and gene content with 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames. A total of 153 repeat sequences were revealed. Forward repeats were dominant, whereas complementary repeats were found only in C. pulvinatus. The mononucleotide SSRs composed of A/T units were most common, and hexanucleotide SSRs were detected least often. Eleven highly variable regions which could be utilized as potential markers for phylogeny reconstruction, species identification or phylogeography were identified within Colobanthus chloroplast genomes. Seventy-three protein-coding genes were used in phylogenetic analyses. Reconstructed phylogeny was consistent with the systematic position of the studied species, and the representatives of the same genus were grouped in one clade. All studied Colobanthus species formed a single group and C. lycopodioides was least similar to the remaining species.

Figure 1

Gene map of the six Colobanthus chloroplast genomes. Genes drawn inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise (indicated by arrows). Differential functional gene groups are color-coded. GC content variations is shown in the middle circle. Gene map was generated with the OrganellarGenomeDRAW (OGDRAW) 1.3.1. (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.)

Figure 2

Comparison of LSC, SSC, and IR boundaries of six Colobanthus chloroplast genomes. Asterisk represents the location of one base shift in IR_A/SSC and SSC/IR_B boundary position; 45 and 1,819 bp values should be replaced by 44 and 1,818 bp for C. subulatus.

Figure 3

Number of repeat types and distribution of repeats in six Colobanthus species. (A) Types of repeats, (B) Location of repeat sequences. F, P, R and C represent forward, palindromic, reverse and complementary repeats.

Figure 4

The distribution and type of simple sequence repeats (SSRs) in cp genomes of six Colobanthus species. (A) Number of different SSRs types. (B) Location of different SSRs in IR, SSC and LSC regions. (C) Distribution of SSR motifs in different repeat class types. (D) Partition of SSRs among IGS, introns and exons.

Figure 5

Sliding window analysis of the eight Colobanthus complete chloroplast genome sequences (window length: 800 bp; step size 50 bp). The Y-axis presents nucleotide diversity of each window, while the X-axis represents position of the midpoint.

Figure 6

Phylogenetic tree based on sequences of sheared 73 protein-coding genes from eight Colobanthus species and 22 other Caryophyllaceae representatives using Bayesian posterior probabilities (PP). Bayesian PP are given at each node.