Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

Abstract

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO₂ concentration conditions at the plateau.

Keywords: Meconopsis; chloroplast genome; high altitude adaptation; high variation region.

Figure 1

The cp genome map of two newly sequenced Meconopsis species, M. paniculata and M. pinnatifolia. The outer circle showed the transcription direction; genes inside were transcribed in the clockwise direction while genes outside were transcribed counterclockwise. LSC/SSC/IR zones were shown in the inner circle. Genes belonging to different functional groups were color coded.

Figure 2

The comparison of the LSC, IR, and SSC border regions among the 12 Meconopsis chloroplast genomes. JLB, JSB, JSA, and JLA denoted the junction sites of LSC and IRb, IRb and SSC, SSC and IRa, and IRa and LSC, respectively. The number above the gene features refers to the distance between the ends of genes and the border sites.

Figure 3

Sequence identity plot comparing the 12 Meconopsis chloroplast genomes with M. pinnatifolia as a reference by using mVISTA. The horizontal axis represents the coordinates of cp genomes in the alignment result. Exons, introns, and conserved noncoding sequences (CNSs) are marked as different colors.

Figure 4

Comparative analysis of the nucleotide polymorphism (Pi) values among the 12 cp genomes of Meconopsis.

Figure 5

Usage preference of amino acids (AAs) and codons for PCGs. (A) AA usage of all the PCGs in each Meconopsis species. (B) RSCU for every AA in M. pinnatifolia. For each amino acid, a color represented a unique codon. (C) ENC-GC3 plot for M. pinnatifolia; each gene was displayed as a dot, and different colors mean genes in distinct functional groups.

Figure 6

Repeats analysis among cp genomes of Meconopsis. (A) Distribution of all repeat units for SSRs in each species. (B) The number of different types of SSRs in each species. (C) Distribution of SSRs, respectively, in LSC, SSC, and IR regions. (D) The number of different types for long repeats.

Figure 7

(A) Maximum likelihood (ML) phylogenetic tree of 58 species, reconstructed with 132 PCGs (bootstrap below 70% are hidden). (B) Bayesian Inference (BI) phylogenetic tree of 58 species, reconstructed with 132 PCGs (bootstrap below 0.7 are hidden). Two non-Papaveraceae species, Epimedium dolichostemon, and Epimedium lishihchenii, were set as outgroups.

Figure 8

Heatmap representing pairwise Ka/Ks ratios of PCGs among the Meconopsis species. The color bias toward red indicates that there is a higher Ka/Ks ratio between genes.