Dataset Information

A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains.

ABSTRACT: Background:Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. Methods:The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. Results:The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.

SUBMITTER: Tyagi S

PROVIDER: S-EPMC7337036 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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A comparative analysis of the complete chloroplast genomes of three <i>Chrysanthemum boreale</i> strains.

Tyagi Swati S Jung Jae-A JA Kim Jung Sun JS Won So Youn SY

PeerJ 20200703

<h4>Background</h4><i>Chrysanthemum boreale</i> Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three <i>C. boreale</i> strains. These were collected from different geographic regions of Korea and varied in floral morphology.<h4>Methods</h4>The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic an ...[more]

PMID: 32685287

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Project description:BackgroundSome ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution.Materials and methodsThe complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes.ResultsThe whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75-108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C-to-U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single-copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships.ConclusionThe results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.

Dataset Information

A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains.

Publications

A comparative analysis of the complete chloroplast genomes of three <i>Chrysanthemum boreale</i> strains.

Similar Datasets

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