Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae)

Abstract

Background Carduus, commonly known as plumeless thistles, is a genus in the Asteraceae family that exhibits both medicinal value and invasive tendencies. However, the genomic data of Carduus (i.e., complete chloroplast genomes) have not been sequenced. Methods We sequenced and assembled the chloroplast genome (cpDNA) sequences of three Carduus species using the Illumina Miseq sequencing system and Geneious Prime. Phylogenetic relationships between Carduus and related taxa were reconstructed using Maximum Likelihood and Bayesian Inference analyses. In addition, we used a single nucleotide polymorphism (SNP) in the protein coding region of the matK gene to develop molecular markers to distinguish C. crispus from C. acanthoides and C. tenuiflorus. Results The cpDNA sequences of C. crispus, C. acanthoides, and C. tenuiflorus ranged from 152,342 bp to 152,617 bp in length. Comparative genomic analysis revealed high conservation in terms of gene content (including 80 protein-coding, 30 tRNA, and four rRNA genes) and gene order within the three focal species and members of subfamily Carduoideae. Despite their high similarity, the three species differed with respect to the number and content of repeats in the chloroplast genome. Additionally, eight hotspot regions, including psbI-trnS_GCU, trnE_UUC-rpoB, trnR_UCU-trnG_UCC, psbC-trnS_UGA, trnT_UGU-trnL_UAA, psbT-psbN, petD-rpoA, and rpl16-rps3, were identified in the study species. Phylogenetic analyses inferred from 78 protein-coding and non-coding regions indicated that Carduus is polyphyletic, suggesting the need for additional studies to reconstruct relationships between thistles and related taxa. Based on a SNP in matK, we successfully developed a molecular marker and protocol for distinguishing C. crispus from the other two focal species. Our study provides preliminary chloroplast genome data for further studies on plastid genome evolution, phylogeny, and development of species-level markers in Carduus.

Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

“…This shows that the reported genomes have certain errors in annotations as stated previously in a detailed study of the family Solanaceae (Amiryousefi et al, 2018a) and the comparative genomics of the two species of Malvaceae . The gene content was found to be the same in all the species of Asteroideae after correction of annotations, which is also in agreement with gene features in the previously reported plastome of other subfamilies such as Cichorioideae, Pertyoideae, and Carduoideae (Jung et al, 2021;Kim et al, 2019;Lin et al, 2019).…”

“…Hence, the plastomes of Asteroideae avoid the rearrangements by a certain mechanism. The GC content of the plastomes was also similar to previous Asteraceae genomes and of other plant lineages, and high GC content was observed in IRs, which might be due to the presence of rRNAs, as they have a GC content of up to 55% (Amiryousefi et al, 2018a;Jung et al, 2021;Kim et al, 2019;Lin et al, 2019;Poczai & Hyvönen, 2017).…”

Distinctive origin and evolution of endemic thistle of Korean volcanic island: Structural organization and phylogenetic relationships with complete chloroplast genome

“…We used five whole chloroplast genomes of Cirsium species available in the NCBI RefSeq database, considering the data validation and updates to reflect current knowledge, to perform comparative analyses. Compared with a previous study of three Carduus species that belong to the same subtribe as Cirsium, which reported nucleotide diversity with an average of 0.003442 and a peak of 0.0171 [63], our study showed that Cirsium species are more stable and conservative than Carduus species. Furthermore, the variation analysis results were consistent with the general feature, such that IR regions in the chloroplast of angiosperm were the most conserved region (S6 Table ).…”

The complete chloroplast genome of Elephantopus scaber L. (Vernonioideae, Asteraceae), a useful ethnomedicinal plant in asia

“… 2017 ), Carduus acanthoides MK652228 (Jung et al. 2021 ), Silybum marianum KT267161 (Shim et al. 2020 ), Cirsium arvense KY562583 (Dann et al.…”