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.

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

“…Four divergent regions are located in LSC (psbK/psbI, trnS/trnG, psbM/trnD, and rps12/clpP), one in SSC (rps15/ycf1), and one in IR (trnV/rps12). Some of these regions have been previously reported in other species cp genomes [37,67]. Such highly variable regions can provide potential molecular markers for the authentication of plants and assist in phylogenetic analysis studies in this genus [70].…”

“…Microsatellites or simple sequence repeats (SSRs) are tandemly repetitive DNA sequences, comprising of one to six (mono-, di-, tri-, tetra-, penta-, and hexa-) repeat nucleotide units. Also known as microsatellites, SSRs are good molecular markers often used in plant species phylogenetics, identification and population genetic studies [58], as they are highly reliable, reproductive, and highly polymorphic [37,44]. They are highly spread in the PCGs, introns, and intergenic regions.…”

“…Plants 2020, 9,296 11 of 19 species cp genomes [37,67]. Such highly variable regions can provide potential molecular markers for the authentication of plants and assist in phylogenetic analysis studies in this genus [70].…”

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

“…In the previous comparative plastome analysis of the 11 Artemisia species, intergenic spacer regions, including ccsA-ndhD, trnH-psbA, ndhG-ndhI, rps18-rpl20, and rps15-ycf1, were identified as mutational hotspots. However, these loci have not been analyzed in the wide range of taxa of the Asteraceae family [40]. Additionally, known core chloroplast barcodes, such as rbcL, matK, rpoB and rpoC1, had low discriminatory power for classification of Artemisia taxa [21][22][23].…”

“…were included (Table 1). Comparative plastome analysis of these species identified mutational hotspots from intergenic spacer regions and showed that the genus Artemisia is a monophyletic genus and is a sister to the genus Chrysanthemum [40]. Additionally, the draft nuclear genome sequence of A. annua [2n = 2x = 18, 1.76 gigabases (Gb)/ 1C] covering 1.74 Gb was reported [41].…”