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

Abstract

<jats:sec> <jats:title>Background</jats:title> <jats:p><jats:italic>Chrysanthemum boreale</jats:italic> Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three <jats:italic>C. boreale</jats:italic> strains. These were collected from different geographic regions of Korea and varied in floral morphology.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>The sizes of the complete chloroplast genomes of the <jats:italic>C. boreale</jats:italic> strains were 151,012 bp (strain 121002), 151,098 bp (strain <jats:uri xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/IT232531">IT232531</jats:uri>) and 151,010 bp (strain <jats:uri xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/IT301358">IT301358</jats:uri>). 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.</jats:p> </jats:sec>

Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis

“…The nucleotide diversity was higher in the LSC and SSC compared to SSC regions and identified the following hypervariable regions across the Calanthe group plastome: trnS-GCU -trnG-GCC , rpoB-trnC-GCA , trnE-UCC -trnT-GGU , rpl32-trnL-UAG , ccsA-ndhD and protein-coding genes psbL, clpP and rpl32. The markedly high divergence observed in these genes and intergenic regions is similar to that observed in other angiosperms [4,64,65] and may be attributed to rapid genome evolution due to higher mutation rates compared to other regions [66].…”

The genus Chrysanthemum: Phylogeny, biodiversity, phytometabolites, and chemodiversity

“…The DNA sequences of seven low-copy nuclear genes and nrITS were combined to reconstruct a time-calibrated phylogeny of subtribe Artemisiinae ( Figure 2 ). In the monophyletic Chrysanthemum group, Chrysanthemum and Ajania were well resolved, agreeing with capitulum morphology and suggesting the low resolving power of cp and ITS markers ( Zhao et al, 2010 ; Hong et al, 2015 ; Tyagi et al, 2020 ; Masuda et al, 2022 ). Within Chrysanthemum , the C. indicum complex and C. zawadskii complex diverged, which temporally coincide with the late Cenozoic uplift of Northern QTP and associated climatic heterogeneity between eastern and central Asia.…”

“…The cp genome with maternal genetic characteristics has the advantages of multi-copy and conservative structure. The combination of cp genome and high-throughput sequencing technology has become an effective means of plant genetic resources research, which facilitates the study of Chrysanthemum classification and genetic resources ( Tyagi et al, 2020 ; Masuda et al, 2022 ). The accumulation of whole genome sequencing data of Chrysanthemum ( Song et al, 2018 ; Nakano et al, 2021 ; van Lieshout et al, 2022 ) and relevant taxonomic groups will enable the comprehensive phylogenomic analyses to reveal the hybridization/polyploidization events leading to the speciation and formation of CM.…”

Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

“…Divergent hotspots play a significant role in species identification and phylogenetic information. Moreover, IR regions often show lower sequence divergence than SSC and LSC regions [67], this probably due to higher mutation rates lead to rapid genome evolution compared to other regions [68]. In our study, this phenomenon was evident that the SSC area showed the maximum nucleotide diversity followed by the LSC region, and the IR regions had the lowest Pi value (Fig.…”