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. 2025 Jun 7;10(7):563–567. doi: 10.1080/23802359.2025.2492133

Characterization of the complete chloroplast genome of Ajania fastigiata (Aasteraceae)

Kalbinur Ghulam a, Guoping Wang c, Ayxamgul Helil a, Buweihailiqiemu Ababaikeri b, Muhammadjan Abduwaki b,✉
PMCID: PMC12147474  PMID: 40492234

Abstract

Ajania fastigiata is a traditional Chinese medicinal plant native to northwestern China. Here, we sequenced and assembled its complete chloroplast genome using Illumina data. The complete chloroplast genome of A. fastigiata is 151,118 bp in length and has a typical quadripartite structure, containing 132 genes (87 protein-coding genes, 37 tRNA, and 4 rRNA). A phylogenetic analysis revealed that A. fastigiata clusters with A. khartensis and A. nematoloba in a well-supported clade with high bootstrap values. The complete chloroplast genome sequence of A. fastigiata may provide valuable genomic resources for studying the systematic evolution of the Asteraceae family.

Keywords: Ajania fastigiata, complete chloroplast genome, phylogenetic analysis

Introduction

The genus Ajania Poljakov belongs to the Asteraceae family (Fu et al. 2016) and comprises approximately 30 species of perennial herbs, semi-shrubs. These species are predominantly distributed in the arid and semi-arid regions of temperate Asia, particularly in China and Japan (Ajania at Flora of China website, http://www.iplant.cn/info/Ajania). Many Ajania species possess significant commercial value and are widely used as fungicides, insecticides, and medicinal remedies, as well as for ornamental purposes. Notable examples include A. pallasiana, A. tenuifolia, and A. fastigiata (Wangchuk et al. 2016).

Ajania fastigiata (C. Winkl.) Poljak. 1955 is a perennial herbaceous plant commonly found in Xinjiang, China, as well as in Afghanistan and Kazakhstan (Li et al. 2021). It is an important medicinal herb extensively used in traditional Chinese medicine to treat coughs, colds, fevers, arthritis, and skin rashes (Ajania at Flora of China website, http://www.iplant.cn/info/Ajania). Previous studies have shown that A. fastigiata contains various bioactive compounds, such as flavonoids, terpenoids, and sesquiterpene lactones. These compounds exhibit pharmacological activities, including anti-inflammatory, anti-tumor, and anti-bacterial properties (Zhao et al. 2010). To facilitate species identification and conservation efforts, obtaining comprehensive genetic information on A. fastigiata is essential. The complete chloroplast genome can serve as a useful molecular marker for exploring the taxonomy and phylogeny of plants, due to its highly conserved structure and moderate mutation rate (Daniell et al. 2016). Previous studies have predominantly focused on the chloroplast genome research of species related to Ajania fastigiata, such as A. ramosa, A. khartensis, and A. nematoloba (Yu et al. 2023). However, its complete chloroplast genome has not been previously reported. In this study, we sequenced and assembled the chloroplast genome of A. fastigiata using whole genome sequencing data from the Illumina platform, and investigated its phylogenetic relationships with closely related species based on whole chloroplast genome sequences.

Materials and methods

Fresh leaves of A. fastigiata (Figure 1) were collected from Kashgar Prefecture (38°45′ N, 75°48′ E), Xinjiang Uygur Autonomous Region, China. A specimen was deposited at college of Xinjiang Uyghur Medicine under the voucher number muhammatjan01 (Muhammadjan Abduwaki: muhammatjan76@163.com). Total genomic DNA was extracted from these leaves using the DNeasy plant tissue kit (TIANGEN Biotech Co., Ltd., Beijing, China). After quality checks, paired-end (PE) sequencing was performed using the Illumina HiSeq 2000 platform at the Kunming Institute of Botany, China (Experiment No. S10190). The complete plastome was assembled using GetOrganelle v1.7.5 (Jin et al. 2020) with the k-mer values set to 21, 43, 65, 87, and 127. Then, the chloroplast genome was annotated with GeSeq v1.59 (Tillich et al. 2017). Further, the start and stop codons of the complete chloroplast genome were edited using Geneious Prime 2022.1.1 (Biomatters Ltd., Auckland, New Zealand). A circular map of the complete plastome and schematic representations of cis- and trans-splicing genes were generated by CPGView software (Liu et al. 2023) (http://www.1kmpg.cn/cpgview/). Simple sequence repeats (SSR) in the A. fastigiata chloroplast genome were identified using the MISA package (Beier et al. 2017) with default parameters.

Figure 1.

Figure 1.

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Morphological characteristics of the A. fastigiata. Morphological characteristics: Herbs, perennial. Stems erect, solitary or fascicled, branched or shortly branched from the Middle or above, pubescent. Florets yellow. Involucres campanulate. Photograph taken by Guoping Wang on June 20, 2023.

For phylogenetic analysis, the complete chloroplast genome of Taraxacum mongolicum (OL875302) was as an outgroup, and those of 17 related taxa from the Asteraceae family were also analyzed together. The optimal nucleotide substitution models for the dataset were determined using PartitionFinder v1.1.1 (Kalyaanamoorthy et al. 2017). Maximum likelihood (ML) analysis was conducted in RAxML‐HPC v8.2.8 on the CIPRES Science Gateway website with 1000 bootstrap replicates (Stamatakis 2014) under a general time-reversible (GTR) model. The consensus trees with branch support were edited in Figtree v1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). Finally, the annotated complete chloroplast genome sequence of A. fastigiata was submitted to the GenBank database of the National Center for Biotechnology Information (NCBI) under accession number OR478164.

Results

The chloroplast genome of A. fastigiata is 151,118 bp in length and has a typical quadripartite structure, comprising a large single-copy region (LSC, 82,918 bp), a small single-copy region (SSC, 18,304 bp), and two inverted repeat regions (IR, 24,948 bp each) (Figure 2). The chloroplast genome has a GC content of 43.1%, similar to other members of the Asteraceae family. A total of 133 genes were identified, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Seventeen genes are duplicated in the IR regions, including 4 rRNA genes, 7 tRNA genes, and 6 protein-coding genes. The cis-splicing genes (Figure S1) and trans-splicing gene rps12 were also identified (Figure S2). The chloroplast genome annotation revealed an average coverage of 110.1×. The sequencing depth and coverage map are presented in Figure S3. In this study, a total of 46 SSRs were detected in the A. fastigiata chloroplast genome. Among these, mono-nucleotide repeats were the most abundant (37 SSRs, accounting for 80.43%), followed by tetra-nucleotides (5 SSRs, 10.64%) and di-nucleotide (4 SSRs, 8.51%) (Table S1).

Figure 2.

Figure 2.

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Chloroplast genome map of A. fastigiata. Genes outside the main circle were transcribed clockwise, while genes on the inside were transcribed counterclockwise. Different colors represent genes with different functions. The gray portion of the inner circle indicates the GC content of the chloroplast genome. LSC: large single-copy region; SSC: small single-copy region; IR: inverted repeat.

A total of 18 complete plastome sequences were analyzed to determine phylogenetic placement of A. fastigiata. The resulting phylogenetic tree revealed four major clades, (Figure 3) strongly supporting the monophyly of the genus Ajania. Within this framework, A. fastigiata was found to be most closely related to A. khartensis and A. nematoloba, forming a well-supported sister group with high bootstrap values.

Figure 3.

Figure 3.

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The maximum likelihood (ML) phylogenetic tree was constructed based on the complete chloroplast genome sequences of A. fastigiata and 18 other closely related plant species, with 1000 bootstrap replicates. The bootstrap support value for each node is shown on the branch. The accession number of the chloroplast genome of each plant species is shown in the brackets. The Artemisia borotalensis NC066237 was downloaded from the publicly available database based on Jin, Wen, et al. (2023); seven sequences Artemisia kaschgarica NC069557, Artemisia schrenkiana NC070206, Artemisia santonicum NC070204, Artemisia leucotricha NC070201, Artemisia ferganensis NC070196, Artemisia karatavica NC070199, Artemisia juncea NC070198 were downloaded from publicly available database based on Jin, Li, et al. (2023); Ajania nematoloba OP723182 was obtained from Yu et al. (2023); Artemisia selengensis ON968865 was obtained from Wang et al. (2024); Artemisia indica ON649707 was obtained from Lan et al. (2022); Artemisia ordosica NC046571 was obtained from Li et al. (2021); artemisia scoparia NC045286, Artemisia brevifolia MT948202 were obtained from Iram et al. (2019); Artemisia desertorum NC063905 was obtained from Chen et al. (2024); Taraxacum mongolicum OL875302 (unpublish).

Discussion and conclusion

This study provides the first complete chloroplast genome sequence of A. fastigiata. Comparisons with others reveal that the genome of A. fastigiata shares structural similarities with that of A. ramosa (151,002 bp), A. przewalskii (151,115 bp), and A. pacifica (151,059 bp) (Yu et al. 2023; Kim and Kim 2020). However, differences in gene content and region lengths suggest distinct evolutionary trajectories among these species.

The identified SSRs offer valuable genetic markers for future population genetics studies. Phylogenetic analysis shows that A. fastigiata clusters closely with A. khartensis and A. nematoloba, forming a well-supported clade within the genus Ajania. This supports using chloroplast genomes as robust tools for resolving evolutionary relationships in Asteraceae (Yu et al. 2010).

The genome sequence provides essential resources for species identification, phylogenetic studies, and functional genomics research, particularly in exploring the bioactive compounds of A. fastigiata. Future work will focus on functional analysis of genes related to medicinal properties and comparative genomics to further elucidate the evolutionary history of Ajania. This study lays a foundation for the conservation and utilization of A. fastigiata in traditional medicine.

Supplementary Material

Supplemental Table S1.xlsx
TMDN_A_2492133_SM4932.xlsx (11.4KB, xlsx)

Acknowledgments

We thank the Molecular Biology Experiment Center, Germplasm Bank of Wild Species in Southwest China, and the National Wild Plant Germplasm Resource Center for providing us with sequencing data. Conceiving and designing, MA; performing and analyzing data, KG, WG, AH, and BA; writing-original draft preparation, MA, KG, WG, AH, and BA; writing-review and editing, MA; KG; WG; AH; and BA; all authors have read and agreed to the published version of the manuscript.

Funding Statement

No funding was received.

Ethical approval

This study did not involve humans or animals. This study did not require ethical approval or permission to collect samples.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under accession no. OR478164 (https://www.ncbi.nlm.nih.gov/nuccore/OR478164). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1014271, SRR25992616, and SAMN37331180, respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplemental Table S1.xlsx
TMDN_A_2492133_SM4932.xlsx (11.4KB, xlsx)

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under accession no. OR478164 (https://www.ncbi.nlm.nih.gov/nuccore/OR478164). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1014271, SRR25992616, and SAMN37331180, respectively.

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