Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots

Abstract

Artemisia L. is among the most diverse and medicinally important genera of the plant family Asteraceae. Discrepancies arise in the taxonomic classification of Artemisia due to the occurrence of multiple polyploidy events in separate lineages and its complex morphology. The discrepancies could be resolved by increasing the genomic resources. A. scoparia is one of the most medicinally important species in Artemisia. In this paper, we report the complete chloroplast genome sequence of Artemisia scoparia. The genome was 151,060 bp (base pairs), comprising a large single copy (82,834 bp) and small single copy (18,282 bp), separated by a pair of long inverted repeats (IRa and IRb: 24,972 bp each). We identified 114 unique genes, including four ribosomal RNAs, 30 transfer RNAs, and 80 protein-coding genes. We analysed the chloroplast genome features, including oligonucleotide repeats, microsatellites, amino acid frequencies, RNA editing sites, and codon usage. Transversion substitutions were twice as frequent as transition substitutions. Mutational hotspot loci included ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1. These loci can be used to develop cost-effective and robust molecular markers for resolving the taxonomic discrepancies. The reconstructed phylogenetic tree supported previous findings of Artemisia as a monophyletic genus, sister to the genus Chrysanthemum, whereby A. scoparia appeared as sister to A. capillaris.

Keywords: Artemisia scoparia; Asteraceae; chloroplast genome; divergence region; phylogenetic; substitutions; taxonomic discrepancies.

Figure 1

Circular map of the Artemisia scoparia chloroplast genome. The genes present outside of the circle are transcribed anti-clockwise, while those inside the circle are transcribed clockwise. Large single copy (LSC), inverted repeat (IRa, IRb), and small single copy (SSC) regions are indicated. The dashed grey color of the inner circle shows the GC content, whereas the lighter gray color shows the AT content. Color of genes was assigned based on their functions.

Figure 2

Details of the contraction and expansion of inverted repeats at junction sites. For all plant species, positive strand genes are represented at the top, from right to left, on the corresponding track, whereas negative strand genes are illustrated on the lower side of the track, from left to right. Arrows depict the distance between the start and end of a gene from the junction site. Scale bar present above or below the genes extending from one region to another illustrates the number of base pairs to which genes join in that region. JSA (SSC/IRa), JSB (IRb/SSC), JLA (IRa/LSC), and JLB (IRb/LSC) indicate the junction sites between two corresponding regions of a genome. The plotted genes and distances surrounding the junction site are a scaled projection of the genome.

Figure 3

The x-axis shows the regions of the chloroplast genome and the y-axis shows the nucleotide diversity of each region. The regions with 0 nucleotide diversity are not included in the list.

Figure 4

Phylogenetic relationships among 30 species of the family Asteraceae. The number on each node represents the bootstrapping value. The bootstrapping values equal to 100 were not represented on the nodes and omitted from the tree for quality visualization.