Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships

Abstract

Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform to sequence three medicinal plants of the Carpesium genus: Carpesium abrotanoides, Carpesium cernuum, and Carpesium faberi, obtaining three complete chloroplast genome sequences after assembly and annotation. It was revealed that the three chloroplast genomes were typical quadripartite structures with lengths of 151,389 bp (C. abrotanoides), 151,278 bp (C. cernuum), and 151,250 bp (C. faberi), respectively. A total of 114 different genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Abundant SSR loci were detected in all three chloroplast genomes, with most composed of A/T. The expansion and contraction of the IR region indicate that the boundary regions of IR/SC are relatively conserved for the three species. Using C. abrotanoides as a reference, most of the non-coding regions of the chloroplast genomes were significantly different among the three species. Five different mutation hot spots (trnC-GCA-petN, psaI, petA-psbJ, ndhF, ycf1) with high nucleotide variability (Pi) can serve as potential DNA barcodes of Carpesium species. Additionally, phylogenetic evolution analysis of the three species suggests that C. cernuum has a closer genetic relationship to C. faberi than C. abrotanoides. Simultaneously, Carpesium is a monophyletic group closely related to the genus Inula. Complete chloroplast genomes of Carpesium species can help study the evolutionary and phylogenetic relationships and are expected to provide genetic marker assistance to identify Carpesium species.

The complete chloroplast genome sequence of Castanopsis fordii Hance (Fagaceae)

“…Accession number: Castanopsis concinna KT793041.1 (Shi et al. 2022 ), Castanopsis hainanensis MG383644.1 (Ogoma et al. 2022 ), Castanopsis fargesii NC_047230.1 (Li et al.…”

“… 2022 ), Lithocarpus balansae KP299291.1 (Shi et al. 2022 ), Castanea henryi KX954615.1 (Shi et al. 2022 ), Castanea mollissima NC_014674 (Jansen et al.…”

“… 2022 ), Castanea henryi KX954615.1 (Shi et al. 2022 ), Castanea mollissima NC_014674 (Jansen et al. 2011 ), Lithocarpus hancei MW375417.1 (Shi et al.…”

“… 2011 ), Lithocarpus hancei MW375417.1 (Shi et al. 2022 ). Castanopsis eyrei and Castanopsis chinensis have no publications and can only cite the sequences by accession numbers.…”

A Comparative Analysis of the Chloroplast Genomes of Three Lonicera Medicinal Plants

“…As a result, cp genome-scale data are increasingly being used to infer phylogenetic relationships at elevated levels of taxonomy, and great progress has been made even in lower taxonomic groups [ 31 ]. The cp genome has haploid genetics, conservative structuring, a comparatively small genome, and a sluggish burst rate of mutations, which makes it an ideally suited model for the molecular identification of species, for studies of genetic diversity, and for revealing phylogenetic relationships [ 32 , 33 , 34 ]. Furthermore, chromatographic fingerprint and Q-Marker content have become important indicators for the identification and quality evaluation of TCM [ 5 , 35 , 36 ], which will greatly increase the accuracy of interspecific identification and provide a reliable basis for the identification and quality evaluation of the herbs in question.…”