Comparison of Four Complete Chloroplast Genomes of Medicinal and Ornamental Meconopsis Species: Genome Organization and Species Discrimination

Abstract

High-throughput sequencing of chloroplast genomes has been used to gain insight into the evolutionary relationships of plant species. In this study, we sequenced the complete chloroplast genomes of four species in the Meconopsis genus: M. racemosa, M. integrifolia (Maxim.) Franch, M. horridula and M. punicea. These plants grow in the wild and are recognized as having important medicinal and ornamental applications. The sequencing results showed that the size of the Meconopsis chloroplast genome ranges from 151864 to 153816 bp. A total of 127 genes comprising 90 protein-coding genes, 37 tRNA genes and 8 rRNA genes were observed in all four chloroplast genomes. Comparative analysis of the four chloroplast genomes revealed five hotspot regions (matK, rpoC2, petA, ndhF, and ycf1), which could potentially be used as unique molecular markers for species identification. In addition, the ycf1 gene may also be used as an effective molecular marker to distinguish Papaveraceae and determine the evolutionary relationships among plant species in the Papaveraceae family. Futhermore, these four genomes can provide valuable genetic information for other related studies.

Figure 1

Chloroplast genome maps of M. racemosa, M. integrifolia (Maxim.) Franch, M. horridula and M. punicea. Genes inside circles are transcribed clockwise, genes outside circles are transcribed counterclockwise. The light gray inner circle corresponds to the AT content, and the dark gray circle corresponds to the GC content. Genes belonging to different functional groups are shown in different colors.

Figure 2

Codon content of twenty amino acids and stop codons in all protein-coding genes of the chloroplast genomes of four Meconopsis species.

Figure 3

Frequency of repeat sequences of the M. racemosa, M. integrifolia (Maxim.) Franch, M. horridula and M. punicea chloroplast genomes determined by REPuter.

Figure 4

Nucleotide variability (%) values between pairs of the four Meconopsis species. (a) Using four species whole genomes; (b) Using four species coding regions.

Figure 5

Sequence identity plot comparing the eight chloroplast genomes with Macleaya microcarpa as a reference by using mVista. Pink bars represent noncoding sequences (CNS), and white peaks represent genomic differences. The y-axis represents the percentage identity (shown: 50–100%).

Figure 6

Phylogenetic tree reconstruction of the 42 species inferred from Bayesian inference (BI) and maximum likelihood (ML) based on 90 protein-coding genes. Numbers above the lines represent BI/ML posterior probabilities.

Figure 7

Phylogenetic tree reconstruction of the 13 species inferred from maximum likelihood (ML), based on the ycf1 genes.