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.
Highlights
IntroductionChloroplast genome sequences have numerous advantages, including low molecular weight, simple structure, uniparental (generally maternal) mode of inheritance, haploidy, highly conserved structure and a slower evolutionary rate of change than nuclear genomes
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
Two papers presented the complete sequence of the chloroplast genomes of C. quitensis[25] and C. apetalus[26], whereas the size of the nuclear genome in C. quitensis was estimated by flow cytometry in only one s tudy[27]
Summary
Chloroplast genome sequences have numerous advantages, including low molecular weight, simple structure, uniparental (generally maternal) mode of inheritance, haploidy, highly conserved structure and a slower evolutionary rate of change than nuclear genomes For this reason, chloroplast genomes constitute valuable data that are relatively easy to handle with source molecular data, support the validation of complex evolutionary relationships and detailed phylogenetic analyses at group, family or even genus level[29,30,31,32]. The published data indicate that the Colobanthus cp genome is typical for angiosperms in terms of size (151,276 bp for C. quitensis and 151,228 bp for C. apetalus) and composition (112 genes) This genome has a conserved quadripartite circular structure with a large single copy (LSC) region, a small single copy (SSC) region and two copies of inverted repeat (IR) regions[43,44]. The genomic data for other members of the genus Colobanthus are still limited
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