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

PeerJ
Swati TyagiSo Youn Won

Abstract

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. 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. 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. Reg...Continue Reading

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Datasets Mentioned

BETA
MG913594
IT232531
IT301358

Methods Mentioned

BETA
electrophoresis

Software Mentioned

Organellar GenoMe Annotator
Baekma
NG
MISA
TREE
tRNAscan
ModelFinder
FigTree
cpGAVAS
ModelTest

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