Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua

Abstract

The complete chloroplast genome of Artemisia annua (Asteraceae), the primary source of artemisinin, was sequenced and analyzed. The A. annua cp genome is 150,995 bp, and harbors a pair of inverted repeat regions (IRa and IRb), of 24,850 bp each that separate large (LSC, 82,988 bp) and small (SSC, 18,267 bp) single-copy regions. Our annotation revealed that the A. annua cp genome contains 113 genes and 18 duplicated genes. The gene order in the SSC region of A. annua is inverted; this fact is consistent with the sequences of chloroplast genomes from three other Artemisia species. Fifteen (15) forward and seventeen (17) inverted repeats were detected in the genome. The existence of rich SSR loci in the genome suggests opportunities for future population genetics work on this anti-malarial medicinal plant. In A. annua cpDNA, the rps19 gene was found in the LSC region rather than the IR region, and the rps19 pseudogene was absent in the IR region. Sequence divergence analysis of five Asteraceae species indicated that the most highly divergent regions were found in the intergenic spacers, and that the differences between A. annua and A. fukudo were very slight. A phylogenetic analysis revealed a sister relationship between A. annua and A. fukudo. This study identified the unique characteristics of the A. annua cp genome. These results offer valuable information for future research on Artemisia species identification and for the selective breeding of A. annua with high pharmaceutical efficacy.

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus acutissima

“…It is obvious that the DNA G + C content of the IR region is higher than that of other regions (LSC, SSC). This phenomenon is very common in other plants [23,24]. GC skewness has been shown to be an indicator of DNA lead chains, lag chains, replication origin, and replication terminals [25,26,27].…”

Complete Chloroplast Genome of Castanopsis sclerophylla (Lindl.) Schott: Genome Structures, Comparative and Phylogenetic Analysis

“…The GC content is highest in the IR regions (42.78%), the phenomena was found in the chloroplast genome of C. hainanensis [30]. The overall GC content is an important indicator of species affinity[31].…”

Comparative Analysis of the Complete Chloroplast Genome of the Alloplasmic Sunflower (Helianthus L.) Lines with Various CMS Types

“…Our results are well consistent with the data from other studies that chloroplast microsatellite loci are mainly represented by short polyT and polyA repeats, which in turn makes a significant contribution to the prevalence of AT nucleobases (62.38-62.40%). As is typical for other flowering plants (Ni et al, 2016;Shen et al, 2017), the most number of polymorphic sites is located in large single copy region; the lowest number of polymorphisms is located in inverted repeat region of chloroplast genomes. Of the 317 SNPs detected, 120 were located in the coding regions.…”