Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives

Abstract

Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.

The haplotype‐resolved genome of diploid Chrysanthemum indicum unveils new acacetin synthases genes and their evolutionary history

“…To elucidate the phylogenetic relationships at the organellar genome level among C. indicum, C. lavandulifolium and C. nankingense, we utilized chloroplast genomes of C. indicum (OQ835564), C. indicum var. aromaticum (OQ835569) from previous studies (Liu et al, 2023), as well as C. lavandulifolium (MW411184.1) and C. nankingense (MT919682.1) downloaded from NCBI. The chloroplast genome of C. zawadskii (MW464197.1) was used as an outgroup.…”

“…Chrysanthemum indicum L., one of the major sources of acacetin (Ma et al, 2018), is a perennial herbaceous medicinal plant with various medicinal properties (Klie et al, 2014;Liu et al, 2023;Luo & Li, 2013). The Chinese Pharmacopoeia (Committee, 2020) describes dried flowers of C. indicum have been utilized in traditional Chinese medicine (TCM) for the treatment of carbuncles, boils, red and swollen eyes, and headaches with dizziness.…”