Comparative chloroplast genomics and phylogenetic analysis of Oreomecon nudicaulis (Papaveraceae)

Abstract

Oreomecon nudicaulis, commonly known as mountain poppy, is a significant perennial herb. In 2022, the species O. nudicaulis, which was previously classified under the genus Papaver, was reclassified within the genus Oreomecon. Nevertheless, the phylogenetic status and chloroplast genome within the genus Oreomecon have not yet been reported. This study elucidates the chloroplast genome sequence and structural features of O. nudicaulis and explores its evolutionary relationships within Papaveraceae. Using Illumina sequencing technology, the chloroplast genome of O. nudicaulis was sequenced, assembled, and annotated. The results indicate that the chloroplast genome of O. nudicaulis exhibits a typical circular quadripartite structure. The chloroplast genome is 153,903 bp in length, with a GC content of 38.87%, containing 84 protein-coding genes, 8 rRNA genes, 38 tRNA genes, and 2 pseudogenes. The genome encodes 25,815 codons, with leucine (Leu) being the most abundant codon, and the most frequently used codon is AUU. Additionally, 129 microsatellite markers were identified, with mononucleotide repeats being the most abundant (53.49%). Our phylogenetic analysis revealed that O. nudicaulis has a relatively close relationship with the genus Meconopsis within the Papaveraceae family. The phylogenetic analysis supported the taxonomic status of O. nudicaulis, as it did not form a clade with other Papaver species, consistent with the revised taxonomy of Papaveraceae. This is the first report of a phylogenomic study of the complete chloroplast genome in the genus Oreomecon, which is a significant genus worldwide. This analysis of the O. nudicaulis chloroplast genome provides a theoretical basis for research on genetic diversity, molecular marker development, and species identification, enriching genetic information and supporting the evolutionary relationships among Papaveraceae.

Keywords: O. nudicaulis; Chloroplast genome; Structural characteristics; Systematic evolution.

Fig. 1

Gene map of the chloroplast genome of O. nudicaulis. The forward-coding genes are located beyond the perimeter of the circle, whereas the reverse-coding genes are located within its center. The inner gray circle symbolizes the GC content

Fig. 2

Frequency of amino acid use in protein-coding genes of O. nudicaulis. The boxes below represent the total RSCU values of all codons encoding each amino acid; the heights of the columns above them represent the total RSCU values of all codons

Fig. 3

Distribution of Repeated Sequences in the Complete Chloroplast Genome of O. nudicaulis. This bar graph displays the length of various repeated sequences (in base pairs) identified within the chloroplast genome of O. nudicaulis. The x-axis represents the length of the repeat sequences, ranging from 30 to 25,680 base pairs. The y-axis denotes the frequency of each repeat length. The types of repeats are classified into Forward (F), Reverse (R), Complement (C), and Palindromic (P) sequences, as indicated by the respective annotations

Fig. 4

Numerical statistics of SSRs in the complete chloroplast genome of O. nudicaulis. This figure presents a bar graph illustrating the distribution of SSRs by length and the number of repeats. The x-axis represents the length of the repeat in base pairs (bp), while the y-axis indicates the number of SSRs found within each length category

Fig. 5

The comparison of Small Single-Copy (SSC), Large Single-Copy (LSC), Inverted Repeat B (IRB), and IRB boundary regions in the chloroplast genomes of Meconopsis henrici (MN488591), Meconopsis horridula (MK533646), Meconopsis integrifolia (MK533647), Meconopsis racemosa (MK533649), O. nudicaulis (MW151698), Papaver dubium (NC_065205), Papaver orientale (NC_037832), Papaver pseudo-orientale (NC_065210), Papaver rhoeas (NC_037831), Papaver somniferum (NC_029434) was conducted. Comparative analysis of junction sites in chloroplast genomes was also performed. The coordinate position of the start or end of each gene from the corresponding junction is shown with arrows. All the genes that integrate from one region of the chloroplast genome to another region are shown with the T bar above or below, indicating the length of base pairs for which the integration of genes has occurred. The junction sites between each corresponding two regions on the genome are denoted as JLA (IRa/LSC), JLB (IRb/LSC), JSA (SSC/IRa), and JSB (IRb/SSC).

Fig. 6

Phylogenetic tree constructed using the maximum likelihood (ML) method based on the complete chloroplast genome sequences of 55 Ranales species. The numbers at the nodes are the bootstrap support values. The heatmap adjacent to the phylogenetic tree displays the protein similarity of various species compared to O. nudicaulis. Protein identities range from 68–100%, indicating the level of similarity each species’ chloroplast genome shares with O. nudicaulis. The tree demonstrates the evolutionary relationships among the Aristolochiaceae, Ranunculaceae, Berberidaceae, Menispermaceae, and Papaveraceae families

Fig. 7

Collinearity analysis of chloroplast genomes related to O. nudicaulis. The figure compares the collinear blocks among the chloroplast genomes of O. nudicaulis and other related species including Papaver orientale (NC_037832), Papaver pseudo-orientale (NC_065210), Papaver rhoeas (NC_037831), Papaver dubium (NC_065205), Papaver somniferum (NC_029434), Meconopsis integrifolia (MK533647), Meconopsis henrici (MN488591), Meconopsis horridula (MK533646), and Meconopsis racemosa (MK533649). The x-axis represents the length of the chloroplast genome in kilobases (kb). Different colored blocks indicate conserved genomic regions, illustrating the synteny and genomic rearrangements among these species