Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants

Abstract

Background Artemisia frigida Willd. is an important Mongolian traditional medicinal plant with pharmacological functions of stanch and detumescence. However, there is little sequence and genomic information available for Artemisia frigida, which makes phylogenetic identification, evolutionary studies, and genetic improvement of its value very difficult. We report the complete chloroplast genome sequence of Artemisia frigida based on 454 pyrosequencing.Methodology/Principal FindingsThe complete chloroplast genome of Artemisia frigida is 151,076 bp including a large single copy (LSC) region of 82,740 bp, a small single copy (SSC) region of 18,394 bp and a pair of inverted repeats (IRs) of 24,971 bp. The genome contains 114 unique genes and 18 duplicated genes. The chloroplast genome of Artemisia frigida contains a small 3.4 kb inversion within a large 23 kb inversion in the LSC region, a unique feature in Asteraceae. The gene order in the SSC region of Artemisia frigida is inverted compared with the other 6 Asteraceae species with the chloroplast genomes sequenced. This inversion is likely caused by an intramolecular recombination event only occurred in Artemisia frigida. The existence of rich SSR loci in the Artemisia frigida chloroplast genome provides a rare opportunity to study population genetics of this Mongolian medicinal plant. Phylogenetic analysis demonstrates a sister relationship between Artemisia frigida and four other species in Asteraceae, including Ageratina adenophora, Helianthus annuus, Guizotia abyssinica and Lactuca sativa, based on 61 protein-coding sequences. Furthermore, Artemisia frigida was placed in the tribe Anthemideae in the subfamily Asteroideae (Asteraceae) based on ndhF and trnL-F sequence comparisons.ConclusionThe chloroplast genome sequence of Artemisia frigida was assembled and analyzed in this study, representing the first plastid genome sequenced in the Anthemideae tribe. This complete chloroplast genome sequence will be useful for molecular ecology and molecular phylogeny studies within Artemisia species and also within the Asteraceae family.

The complete chloroplast genome sequences of Artemisia gmelinii andArtemisia capillaris (Asteraceae)

“…Previous studies have reported that A. gmelinii and A. capillaris contain useful metabolites with various pharmacological effects such as anti-infective and anti-oxidant activity and hepatoprotective and antifibrotic effects (K€ oncz€ ol et al 2012;Wang et al 2012). However, to date, genetic and genome research related to barcoding system lack in Artemisia genus, despite the importance of herbal medicine authentication system is increased (Liu et al 2013;Lee et al 2016). In this study, we Figure 1.…”

“…The highquality paired end sequences of 2.1 and 1.6 Gb were generated from A. gmelinii and A. capillaris, respectively, and separately assembled using CLC genome assembler (v. beta 4.6, CLC Inc., Lyngby, Denmark). Afterwards, contigs representing chloroplast sequence were retrieved, ordered and combined into a single draft sequence by comparing chloroplast genomes of A. frigida (JX293720, Liu et al 2013) and A. fukudo (KU360270, Lee et al 2016). The complete genome of A. gmelinii and A. capillaris were deposited in GenBank (A. gmelinii: KU736962 and A. capillaris: KU736963).…”

Complete chloroplast genome sequence of Artemisia fukudo Makino (Asteraceae)

“…We isolated DNA from leaf tissues and performed whole genome shotgun sequencing using an Illumina Miseq platform (Illumina, San Diego, CA). High-quality paired end reads of 1.2 Gb were assembled using CLC genome assembler 4.6 (CLC Inc., Aarhus, Denmark) and contigs representing chloroplast sequence were retrieved, ordered, and combined into a single sequence, by the guidance of chloroplast genome of A. frigida (JX293720) (Liu et al 2013).…”

Complete chloroplast genome sequence of cultivated Morus L. species

“…The expansion and contraction of IR are common evolutionary events in plants (Liu et al, 2013). It is believed that the locations of SSC/IR and LSC/IR junctions are markers of chloroplast genome evolution (Zhang et al, 2013).…”