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.

The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

“…A total of 52 and 53 RNA editing sites were predicted in 18 chloroplast genes of G. sinensis and G. japonica , respectively (Supplementary Tables S3 – S4 ). Among these sites, the highest frequency of amino acid conversion involved serine (S) to leucine (L), which concurs with previous investigations in the chloroplast genomes of higher plant 44 . As previously reported, the number of shared editing sites increases in closely related taxa 45 .…”

Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

“…The hot region of trnE-trnT was matched with the study of Zhao et al (2018) [77]. Although rps16 and its intergenic spacer with trnQ were suggested in much research [10,11,26,74,81], our study introduced a new intergenic spacer of this gene, i.e., rps16-matK. However, searching for new variable sites as candidate barcodes is just the first step.…”

“…Because of this, an understanding of genomics plays a crucial role. Divergent and conserved regions in the genome provide useful information to establish DNA-based [10][11][12][13][14] as well as PCR-based [13,[15][16][17][18][19][20] identification markers, supporting the protection and management of species. However, in Orchidaceae, most of the studies are of the Epidendroideae subfamily.…”

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

“…The extent and types of genetic polymorphisms in different regions of the cp genome vary. In most plants, the single copy regions (LSC and SSC regions) of the cp genome are more variable than that are the IR regions [ 16 , 41 , 42 ]. In our study, nucleotide diversity, as quantified by Pi values across the six Desmodieae cp genomes, for SSC and LSC was 0.02752 and 0.02146, respectively, both of which were significantly higher than the Pi value for the IR regions (0.00374).…”