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Comparative and phylogenetic analysis of the complete chloroplast genomes of 10 Artemisia selengensis resources based on high-throughput sequencing

BMC Genomics volume 25, Article number: 561 (2024) Cite this article

Abstract

Background

Artemisia selengensis, classified within the genus Artemisia of the Asteraceae family, is a perennial herb recognized for its dual utility in culinary and medicinal domains. There are few studies on the chloroplast genome of A. selengensis, and the phylogeographic classification is vague, which makes phylogenetic analysis and evolutionary studies very difficult.

Results

The chloroplast genomes of 10 A. selengensis in this study were highly conserved in terms of gene content, gene order, and gene intron number. The genome lengths ranged from 151,148 to 151,257 bp and were typical of a quadripartite structure with a total GC content of approximately 37.5%. The chloroplast genomes of all species encode 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Due to the contraction and expansion of the inverted repeats (IR), the overlap of ycf1 and ndhF genes occurred at the inverted repeats B (IRB) and short single copy sequence (SSC) boundaries. According to a codon use study, the frequent base in the chloroplast genome of A. selengensis’ third codon position was A/T. The number of SSR repeats was 42–44, most of which were single nucleotide A/T repeats. Sequence alignment analysis of the chloroplast genome showed that variable regions were mainly distributed in single copy regions, nucleotide diversity values of 0 to 0.009 were calculated by sliding window analysis, 8 mutation hotspot regions were detected, and coding regions were more conserved than non-coding regions. Analysis of non-synonymous substitution (Ka) and synonymous substitution (Ks) revealed that accD, rps12, petB, and atpF genes were affected by positive selection and no genes were affected by neutral selection. Based on the findings of the phylogenetic analysis, Artemisia selengensis was sister to the genus Artemisia Chrysanthemum and formed a monophyletic group with other Artemisia genera.

Conclusions

In this research, the present study systematically compared the chloroplast genomic features of A. selengensis and provided important information for the study of the chloroplast genome of A. selengensis and the evolutionary relationships among Asteraceae species.

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Background

Asteraceae is the first family of dicotyledonous plants, currently, there are about 1000 genera and 25,000–30,000 species in the family, and there are about 200 genera and more than 2000 species in China, which are distributed all over the country [1, 2]. As the largest genus in Asteraceae [3], Artemisia has about 300 species. It is mainly found in temperate, cold-temperate, and subtropical regions of Asia, Europe, and North America. In many countries, most Artemisia plants are used as herbal medicines. For example, A. annua is used as a treatment for malaria because of its rich content of artemisinin [4]; the Dragon Boat Festival, a traditional Chinese festival, uses. argyi to repel insects and kill viruses. As a perennial herb of the genus Artemisia in the family Asteraceae, A.a selengensis has rhizomes, young stems are green or purple, young leaves are mostly light green, and old leaves are dark green. The leaves are mostly oval or lance-shaped in shape, with white tomentum on the back, and the whole plant grows upright or obliquely upward. The plant itself has a clear fragrance, the stalks are crisp and tender, rich in protein, fatty acids, and trace elements [5], with a delicious flavor and rich nutrition, and is widely grown mainly as a vegetable in China. A. selengensis contains various chemical substances such as flavonoids, chlorogenic acid, and reducing sugars. It is the polysaccharides, chlorogenic acid, and other bioactive components present within the plant, that have demonstrated effects in anti-tumor, antioxidant and free radical scavenging [6,7,8], which can improve liver function [8] and lower blood sugar [9]. It is also used in tea making, yogurt fermentation, functional shampoos, and cosmetics development [10, 11].

Chloroplasts are important organelles with independent genetic material and capable of photosynthesis, commonly found in terrestrial plants, algae, and a few protists [12, 13], showing matrilineal inheritance in most angiosperms. The chloroplast genomes are relatively conserved in structure [14] and has a typical tetrad structure of a circular genome with a genome size ranging from 120 to 160 kb [15], including a large single-copy region (LSC), a small single-copy region (SSC), and these two single copy regions are separated by two inverted repeat regions (IR), where the inverted repeat regions are pairs of repeats with equal length and opposite orientation sequences [16]. Chloroplast genomes are so commonly used in angiosperms, gymnosperms, and ferns for phylogenetic and comparative genomic investigations [17]. Chloroplast genomes are inherited either paternally or maternally and may be utilized as a legitimate barcode for species identification as well as the creation of additional possible identifying markers [18].

Artemisia species are diverse, complicated in genetic relationships, and have ambiguous taxonomic relationships based on morphology. As organelle genomes with highly conserved genetic information, the chloroplast genomes are widely used for genome evolution studies [19, 20]. Many researchers have used single gene data (accD, ycf1, rbcL, matK, ndhF, rps11) and IGS data (psbA-trnH, trnS-trnC, trnS-trnfM, trnL-trnF) for phylogenetic analysis of Artemisia [21,22,23,24,25,26,27], however, these chloroplast single-gene molecular markers do not work for all plant taxa and only supply limited information at the subspecies level [28]. In contrast, there is little information on the chloroplast genomes of A. selengensis in the current database, and it is unclear whether the chloroplast genomes of A. selengensis resources differ from one region to another. Therefore, in this work, chloroplast whole-genome sequencing, assembly, and annotation of 10 A. selengensis materials from 6 regions using second-generation sequencing technology not only enriched the existing genetic information of the chloroplast genome of A. selengensis, which was helpful for phylogenetic and taxonomic studies but also provided genetic information for the conservation of A. selengensis germplasm resources. To better understand the evolution of the chloroplast genome structure of A. selengensis and to clarify the evolutionary relationships between A. selengensis and other Artemisia species, genome structure analysis and comparative genomic research were also carried out.

Methods

Samples collection

Ten A. selengensis germplasm resources were collected from 6 provinces in China. The material’s number, source, and GenBank number are listed in Table 1. The labels for 10 different A. selengensis materials were HWB, HWS, HQ, HY, HC, JN1, JN2, AC, JS, and YN.

Table 1 Ten germplasm resources of A. selengensis from six provinces
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Chloroplast genome sequencing

More than 0.5 g of fresh leaves were taken from each material separately, kept in discolored silica gel, and then sequenced by Illumina high-throughput sequencing platform from Beijing Novogene Biotechnology Co., Ltd. A total of 56.5 G of raw data and 56.15 G of filtered clean data were generated by sequencing. The clean data were utilized to assemble the chloroplast complete genome. The base quality values of the sequencing results were all above 97% for Q20 and above 92% for Q30 (Supplementary Table S1).

Genome assembly and annotation

In this study, the chloroplast genomes of A. selengensis were assembled using GetOrganelle v1.7.5.3 software [29]. We used the published complete chloroplast genome of A. selengensis downloaded from NCBI [30] (GenBank accession: NC_039647) as a reference for chloroplast genome annotation of 10 A. selengensis materials, using CPGAVAS2 (http://www.herbalgenomics.org/cpgavas) online software and PGA software [31] to annotate the chloroplast genomes of A. selengensis. By using Geneious v8.0.4 software [32], we compared the number of annotated chloroplast genome genes, added missing genes manually, verified the CDS sequences rigorously, and manually modified the start codon and stop codon of the misannotated genes. If a gene was present as a shortened partial copy of another gene or had an internal stop codon in comparison to other homologous genes, it was deemed to be a pseudogene. The annotated GenBank file was converted into a five-column tab-delimited annotation file using GB2Sequin [33], and the chloroplast genome annotation files and the complete FASTA sequence files for 10 materials were submitted to GenBank via Bankit and specific accession numbers were acquired (Table 1). The annotated chloroplast genomes were visualized using the online software Chloroplot (https://irscope.shinyapps.io/Chloroplot).

Structural characterization and comparative chloroplast genome analysis

Geneious v8.0.4 software was used to calculate the whole genome length, length of each region (large single-copy region, small single-copy region, inverted repeats), gene composition and position distribution, base composition, and GC (AT) content to analyze the characteristics of the chloroplast genomes of A. selengensis.

Boundary regions and comparative analysis

Variations in gene sequences at the boundary junctions of the 4 regions are observed across different plant species. The main reason for the variation in chloroplast genome length is the expansion and contraction of the IR region. We used the CPJSdraw-boundary map drawing tool (http://cloud.genepioneer.com:9929) of the JSHYCloud Platform to analyze and compare the boundary regions between the large single-copy region (LSC) and the IR region and between the small single-copy region (SSC) and the IR region.

Codon usage analysis

Codon usage bias (CUB) refers to the phenomenon that codons have the characteristics of degeneracy in the process of gene translation between different species or within the same species, that is, one amino acid corresponds to different codons, resulting in some codons using more than other synonymous codons [34]. CUB is a useful tool for understanding genetic and evolutionary processes, and the analysis of codon usage bias in genes can help determine these genes’ origin and evolutionary history. In this study, CodonW software was used to analyze the codon preferences and the results were visualized for graphing using R software. By employing CodonW and CUSP software, we calculated the effective number of codons (ENC), relative synonymous codon usage (RSCU), and the overall GC content (GCall) for each gene. Concurrently, the GC content at the three positions of codons was recorded, denoted as GC1, GC2, and GC3, respectively, with the GC content at the third position of synonymous codons represented as GC3s. To reduce errors, protein-coding sequences needed to be screened, requiring each CDS sequence to be a multiple of 3, ≥ 300 bp in length, each containing a start codon and a stop codon, with no stop codon inside the sequence, while duplicate sequences were removed, and finally, all 53 CDS sequences were retained for codon analysis.

Scattered repeats sequence and SSRs analysis

Forward, reverse, complementary and palindromic repeats in the chloroplast genome of A. selengensis were detected using the REPuter (https://bibiserv.cebitec.uni-bielefeld.de/reputer) with parameters set to Hamming distance of 3, maximum calculated repeats of 50 and repeat size > 30 bp. Simple sequence repeats (SSR) were detected using MISA (https://webblast.ipk-gatersleben.de/misa/index.php) with nucleotide motifs of 1–6, parameters using default values, and the minimum number of repeats for single nucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide is set to 10, 6, 5, 5, 5 and 5 respectively.

Comparative genomic analysis

Comparing chloroplast genome sequences provides a reference for discovering sequence variants and identifying mutation hotspot regions, as well as detecting gene loss and duplication events. Mutation hotspot regions obtained from chloroplast genome sequences can also be used as effective molecular markers for species identification and population genetics [35, 36]. mVISTA is an online tool for multiple DNA sequence alignment that allows sequence similarity to be assessed by comparing coding and non-coding regions, introns, and exons [37]. In this study, the whole chloroplast genomes of 10 A. selengensis were compared and visualized using mVISTA (http://genome.lbl.gov/vista/index.shtml). The published genome of A. selengensis (NC_039647) was selected as a reference, and the input files were the original FASTA format nucleotide sequence files and gff3 format annotation files. Nucleotide diversity (PI) was calculated using DnaSP v6 software [38], with the window length set to 600 bp and the step size set to 200 bp.

Ka/Ks analysis

We calculated Ka, Ks, and Ka/Ks ratios of homologous protein-coding genes in the chloroplast genomes of A. selengensis and eight other Asteraceae species, including intra-genus species (A. argyi, A. annua, A. absinthium, A. borotalensis) and intergeneric species (other genera of Asteraceae: A. carlinoides, Chrysanthemum vestitum, Aster albescens, Helianthus carnosus). The GenBank file was downloaded from NCBI, the protein-coding sequences in the GenBank file were extracted, and the homologous protein sequences were obtained by comparing other protein sequences with the reference protein sequences using BlastN (v2.10.1) to find the best match; then the homologous protein sequences were automatically aligned using MAFFT (v7.427) software [39], and the aligned protein sequence was mapped to the coding sequence to obtain the aligned coding sequence. Finally, the KaKs_Calculator2 software [40] was used to calculate the non-synonymous substitution rate (Ka), the synonymous substitution rate (Ks), and their ratios using the YN method. Ka/Ks > 1 indicates positive selection, Ka/Ks < 1 indicates purifying selection, and Ka/Ks = 1 denotes neutral selection.

Phylogenetic analysis

The complete chloroplast genome GenBank data of 27 published genera of Artemisia and other genera in the Asteraceae family were downloaded from NCBI and phylogenetically analyzed with the 10 A. selengensis materials in this study, and the species names and GenBank accession numbers of the chloroplast genomes downloaded from NCBI are listed in Table S2 (Supplementary Table S2). Protein-coding sequences homologous and non-coding regions to the chloroplast genome were extracted for phylogenetic tree construction. The shared protein-coding sequences and non-coding regions were extracted using PhyloSuite software [41], and sequence alignment were performed using MAFFT. The compared sequences were then trimmed and concatenated and finally imported into IQTree to find the best model and construct a phylogenetic tree using the maximum likelihood method.

Results

Chloroplast genome structure and features

In terms of gene content, gene order, and the number of gene introns, the 10 A. selengensis materials included in this study’s research had substantially conserved chloroplast genomes. The genome lengths ranged from 151,148 to 151,257 bp, and all had a typical tetrameric loop structure containing four regions, LSC, SSC, IRA, and IRB (Fig. 1). the LSC region was 82,888 to 82,956 bp in length, the SSC region was 18,338 to 18,390 bp in length, and the IR region was 24,961 to 24,964 bp in length. The total chloroplast genome GC content of the 10 materials was about 37.5%, showing a high degree of similarity. However, the GC content differed among the three major regions of the chloroplast genome, and the GC content of the IR region was 43.1%, which was higher than that of the LSC region (35.6%) and the SSC region (30.8%) (Supplementary Table S3).

Each chloroplast genome contains 133 genes, the number of protein-coding genes, tRNA genes, and rRNA genes are 88, 37, and 8, respectively (Table 2, Table SS3). The chloroplast genome contained 17 intron genes, including 11 protein-coding genes and 6 tRNA genes. Fifteen genes contained one intron and 2 genes (ycf3 and clpP) contained two introns (Table 3). the LSC location included 68 protein-coding genes and 28 tRNA genes, the IR region contained 8 protein-coding genes, 8 tRNA genes, and 8 rRNA genes, and the SSC region contained 12 protein-coding genes and 1 tRNA gene. The genes in the LSC region accounted for 72.2% of the chloroplast genome, the IR region for 18.0%, and the SSC region for 9.8%.

Fig. 1
figure 1

Complete chloroplast genome map of A. selengensis. In the lower-left corner is the legend, which classifies chloroplast genes according to their different functions. Genes on the outside of the circles are transcribed in a counterclockwise direction, and those on the inside of the circles are transcribed in a clockwise direction. The inner circle’s dark gray represents the distribution of GC content, while the outside circle’s light gray represents the distribution of AT content

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Table 2 Predicted genes in the chloroplast genome of A. selengensis
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Table 3 Location and length of exon and intron genes in the chloroplast genome of A. selengensis
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IR boundary analysis

The IR region is one of the most conserved regions in the plant chloroplast genome, and the contraction and expansion of the IR region is the main cause of changes in chloroplast genome size and gene number, as well as a common evolutionary event in the chloroplast genome [35, 36]. Therefore, we performed boundary region analysis of the chloroplast genomes of 10 A. selengensis materials, and the results showed that the boundaries of the four regions were relatively conserved, and the types and numbers of genes in the boundary regions were highly consistent (Fig. 2). The contraction and expansion of the reverse repeat region showed high similarity at the boundary junctions of LSC/IRB, IRB/SSC, SSC/IRA, and IRA/LSC. The boundary of LSC/IRB was located at the rps19 gene, which was 212–218 bp in the LSC region and 61–67 bp in the IRB region. The ycf1 and ndhF genes were located at the SSC/IR region boundary, and the IRB/SSC boundary is located in the ycf1 gene, which extends 558 bp into the IRB region and 36–108 bp into the SSC region. The trnN-GUU genes are all located in the IRA region at the SSC/IRA boundary, rpl2 genes are completely present in the IRB region at the LSC/IRB boundary, and the trnH-GUG gene was located in the LSC region. In addition, we also found that the ycf1 and ndhF genes overlapped at the IRB/SSC boundary in the A. selengensis material (HWB) from Baishazhou (HWB) and Shamao (HWS) in Wuhan City, Hubei Province. The location and order of the genes in the border area were largely constant in all materials, showing that the IR region is highly conserved.

Fig. 2
figure 2

Comparison of chloroplast genome boundary regions of 10 A. selengensis

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Codon usage analysis

The base composition and GC content of the chloroplast genomes of the 10 A. selengensis materials in this study were identical, and we selected A. selengensis materials from Baishazhou, Wuhan, Hubei Province, to analyze the frequency of codon usage. The analysis of codon usage showed that a total of 20 amino acids (excluding stop codons) were encoded, with a frequency of 1.1-10.8% for each amino acid. Arginine, leucine, and serine were the most abundant amino acids, and cysteine was the least used (1.1%). Among the amino acids encoded, all amino acids were encoded by two to six codons except methionine and tryptophan, which were encoded by one codon (Fig. 3). The results showed that arginine, leucine, and serine were all encoded by six synonymous codons, of which the most frequently used codons were CGT, TTA, and TCT. Four synonymous codons were used to encode the amino acids alanine, glycine, proline, threonine, and valine. The most common codons were GCT, GGT, CCT, ACT, and GTT. Isoleucine contained three synonymous codons, with ATT being the most commonly used codon. Asparagine, aspartic acid, cysteine, glutamine, glutamate, histidine, lysine, phenylalanine, and tyrosine were encoded by two synonymous codons that were employed at about the same frequency. The most frequently used codons for each of these nine amino acids were AAT, GAT, TGT, CAA, GAA, CAT, AAA, TTT, and TAT. In the chloroplast genome of A. selengensis, there were 29 codons with RSCU > 1, 28 of which ended in A/T, accounting for 96.55%. 30 codons with RSCU < 1, 28 of which ended in G/C, accounting for 90.63%. The starting codons AUG and UGG were both unbiased codons (RSCU = 1). The findings revealed that the common base in the third position of the codon in A. selengensis’ chloroplast genome was A/T. The ATG codon used methionine encoding formylmethionine as the start codon. This is the most common start codon in the chloroplast genomes of all species. However, other codons have been found as start codons during translation, such as GTG (rps19), and ACG (psbL).

Fig. 3
figure 3

The amino acids’ Codon content encodes proteins in the chloroplast genome of A. selengensis

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To clarify the codon usage bias of the chloroplast genomes in ten A. selengensis samples, ENC-plot analysis, PR2-plot analysis, and neutrality plot analysis were conducted concurrently. As indicated in Table 4, the overall GC content (GCall) of the chloroplast protein-coding genes in the ten A. selengensis samples is essentially the same, with the GC content at the first (GC1), second (GC2), and third (GC3) codon positions all being less than 50%. There are differences in the GC content across these three positions, with a decreasing trend observed from the first to the third position, indicating a pattern of GC1 > GC2 > GC3. This indirectly reflects a predominance of A and T bases in the chloroplast genomes of the ten A. selengensis samples, with the bases at the third codon position generally being A or T. As observed in Table 4, the average ENC (Effective Number of Codons) values for ten A. selengensis samples ranged from 49.018 to 49.035, all significantly higher than 35%, indicating that the overall codon bias in the chloroplast genomes is relatively weak.

Table 4 Analysis of codon usage of 10 chloroplast genome protein coding sequences of A. selengensis
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ENC-plot analysis

Figure 4 reveals a high degree of consistency in the ENC-plot results for the chloroplast genomes of ten A. selengensis samples. Most genes are distributed on both sides of the curve, with a greater concentration of genes below the curve. The distribution of some genes along the standard curve indicates that their actual ENC values are close to the expected ones, suggesting that base mutations play a primary role in influencing codon usage bias. Conversely, genes deviating from the standard curve show significant differences between their actual and expected ENC values, indicating that in addition to the influence of base mutations, natural selection also affects codon usage bias.

Fig. 4
figure 4

ENC-plot analysis of 10 A. selengensis chloroplast genomes. Note a ~ j A. selengensis germplasms in the figure are Wuhan Baishazhou, Wuhan Shamao, Qichun, Hunan Yueyang, Hunan Chenzhou, Jiangsu Nanjing 1, Jiangsu Nanjing 2, Anhui Chuzhou, Jiangxi Shangrao and Yunnan

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PR2-plot analysis

From Fig. 5, it is evident that genes are randomly distributed across four regions, with most points situated far from the center, and the majority located in the bottom-right TG region. This overall distribution indicates a scenario where the third position base of codons is predominantly T > A and G > C, suggesting that the bias in the usage of the third base of codons in the chloroplast genomes of the ten A. selengensis samples is mainly influenced by natural selection.

Fig. 5
figure 5

PR2-plot analysis of 10 A. selengensis chloroplast genomes. a–j A. selengensis germplasms in the figure are Wuhan Baishazhou, Wuhan Shamao, Qichun, Hunan Yueyang, Hunan Chenzhou, Jiangsu Nanjing 1, Jiangsu Nanjing 2, Anhui Chuzhou, Jiangxi Shangrao and Yunnan

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Neutrality plot analysis

To analyze the impact on codon usage bias in the chloroplast genomes of ten A. selengensis samples, the average value of GC content at the first and second positions of codons (GC12) was plotted on the y-axis, and the GC content at the third position (GC3) was plotted on the x-axis. As indicated in Fig. 6, the GC12 values of the codons in the chloroplast genomes of the ten A. selengensis samples mainly range between 30.14 and 56.2, while the GC3 values are distributed between 23.03 and 25.55, demonstrating a higher frequency of A/T base usage at the third codon position. The slope of the fitted curve ranges from 0.1579 to 0.1797, with a regression coefficient (R2) greater than 0, indicating a positive correlation between GC12 and GC3, albeit not significant. This also suggests that the codon usage in the chloroplast genomes of the ten A. selengensis samples differs between the mutations patterns at the first and second positions and the third, with the codon usage bias at the first and second positions being more influenced by natural selection.

Fig. 6
figure 6

Neutrality plot analysis of 10 A. selengensis chloroplast genomes. a–j A. selengensis germplasms in the figure are Wuhan Baishazhou, Wuhan Shamao, Qichun, Hunan Yueyang, Hunan Chenzhou, Jiangsu Nanjing 1, Jiangsu Nanjing 2, Anhui Chuzhou, Jiangxi Shangrao and Yunnan

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Scattered repeat sequence and microsatellite (SSR) analysis

Scattered repetitive sequences can be generally classified into four types: forward repeats, reverse repeats, complementary repeats, and palindromic repetitive sequences. In this study, 42–45 repetitive sequences were detected in 10 materials by REPuter, which contained 22–24 forward repeats, 19–20 palindromic repeats, and 0–3 reverse repeats, and no complementary repeats were detected in all materials. The abundance of repetitive sequences varied depending on the repetitive sequence type, with forward repeats exhibiting the greatest abundance among all materials, followed by palindromic repeats (Fig. 7a). The minimum length of these repetitive sequences was at least 30 bp and the maximum was 72 bp, and most of the repetitive sequences were distributed in the range of 30–44 bp in length (Fig. 7b). Among the four regions, the IR region contained more repetitive sequences than the LSC and SSC, while some repetitive sequences were also shared between different regions of the chloroplast genome (Fig. 7c).

Fig. 7
figure 7

Type and distribution of scattered repeats in 10 A. selengensis. (a) Types and numbers of the four repeats. (b) Distribution of the sizes of the repetitive sequences. (c) Distribution of repetitive sequences in the three major regions of the chloroplast genome

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The chloroplast genomes of 10 materials were detected with SSR loci using MISA. The results showed that the number of cpSSRs ranged from 42 to 44 (Fig. 8a), with the least number of SSR loci detected for A. selengensis (HY) from Yueyang City, Hunan Province, with 42 SSR loci, the most SSR loci detected for A. selengensis (AC) from Chuzhou City, Anhui Province, with 44 loci, and 43 SSR loci detected for the remaining eight materials. Single nucleotide repeats were the most abundant in all materials, consisting mainly of polyadenine (ploy-A) and polythymine (ploy-T), followed by dinucleotide repeats AT/TA, and rarely containing tandem guanine (G) or cytosine (C) (Fig. 8b). In addition, we did not find a large number of trinucleotide to tetranucleotide repeats. SSR repeats were randomly distributed in the chloroplast genome (Fig. 8c), with 339 in LSC, 58 in SSC, and 22 in IR regions (310 in spacer regions, 59 in introns, and 50 in exons). The results showed that most of the SSRs were distributed in the LSC region and the spacer region (Fig. 8d).

Fig. 8
figure 8

Type and distribution of chloroplast genomic SSRs in 10 A. selengensis. (a) Number of SSR repeat types. (b) Number of identified SSR motifs in different repeat types. (c) Frequency of SSR occurrence in LSC, SSC, and IR regions. (d) Percentage distribution of SSRs in IGS, Intron, and Exon

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Comparative genomic analysis

In this study, we used the online software mVISTA to perform sequence alignment analysis of the complete chloroplast genomes of ten A. selengensis materials, using the NCBI-published Dongting Lake A. selengensis (NC_039647) as a reference. The results showed that the nucleotide sequence similarity of the ten chloroplast genomes was extremely high, and the genomes showed a high degree of covariance with each other, indicating their evolutionary conservation at the genome level (Fig. 9). After comparative analysis, we found that IR regions and coding regions were more conserved than non-coding regions. More variation in the chloroplast genome occurs in the non-coding regions (CNS), where the non-coding regions with high levels of variation are petN-psbM, trnR-UCU-trnG-UCC, and rpl32-trnL-UAG, which can be used for phylogenetic studies [42, 43]. Variable regions have also been found in some coding genes, such as accD, rps19, and ndhA, and differences in accD and ycf1 have been found in other angiosperm plastid genomes [24, 44,45,46], making these genes also reliable markers for phylogenetic analyses [47].

Fig. 9
figure 9

Sequence alignment analysis of the chloroplast genomes of 10 A. selengensis in this study using mVISTA software, using the Dongting Lake chloroplast genome sequence as a reference. The x-axis represents the coordinates of the chloroplast genome. The y-axis indicates the average percentage of identity within 50–100%. The direction of gene transcription is indicated by gray arrows, and the genomic regions are color coded for exons, tRNA, rRNA, conserved non-coding sequences, and mRNA

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In addition, to further assess the sequence divergence of the chloroplast genome of A. selengensis, we calculated the nucleotide diversity of the chloroplast genome of 10 A. selengensis materials with other Artemisia species (A. fukudo, A. annua, A. argyi, and A. capillaris) using DNAsp software. The analysis indicated that the nucleotide diversity varied from 0 to 0.009 within a sliding window length of 600 base pairs, with the IR area having the lowest nucleotide diversity and the SSC region having the greatest nucleotide diversity. By analyzing the calculated nucleotide diversity, a total of eight mutation hotspot regions were detected (Fig. 10), while rpl32-trnL, ndhF-rpl32, and ycf1 sequence intervals each had two mutation hotspot regions inside the interval. Among them, rpl32-trnL had the highest Pi value (Pi = 0.00844). This was followed by four other mutation hotspot regions, including ndhF-rpl32, trnK(exon1), accD, and ycf1; most of these mutation hotspots were located in the SSC region.

Fig. 10
figure 10

Sliding window analysis of the whole chloroplast genome. Sliding window analysis between 10 A. selengensis and other Artemisia species. Sliding window length: 600 bp; step size: 200 bp. X-axis: position of the sliding window. Y-axis: nucleotide diversity of each window

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Ka/Ks analysis of protein-coding genes

Low rates of evolution were seen in the rates of synonymous substitutions (Ks), non-synonymous substitutions (Ka), and their ratios (Ka/Ks) in the chloroplast genome. Synonymous substitutions were more common than nonsynonymous substitutions (Fig. 11), thus, most genes had lower Ka/Ks values, which were affected by the effect of purifying selection. The average Ka value between A. selengensis and four Artemisia plants was 0.1359, and the average Ks value was 0.2313, according to the comparative study of homologous protein-coding genes; the average Ka value between A. selengensis and four other Asteraceae species genera was 0.6861 and the average Ks value was 4.1240. Meanwhile, we also calculated the Ka/Ks ratio to assess the effect of selective pressure on protein-coding genes. In this study we found that within the genus Artemisia, accD, rps12, and petB genes evolved under positive selection pressure with Ka/Ks > 1; between genera atpF gene and rps12 gene with Ka/Ks > 1 showed positive selection pressure. No neutral selective effect was found (Supplementary Table S4).

Fig. 11
figure 11

Ka/Ks analysis of homologous protein-coding genes in the complete chloroplast genomes of eight Asteraceae species and A. selengensis

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Phylogenetic analysis

Using 81 homologous protein-coding sequences, we performed a phylogenetic analysis of 10 A. selengensis materials and 27 other Asteraceae plants by the maximum likelihood method with the best model of TVM + F + R2 (Fig. 12), and the results yielded well-supported tree topologies. Among the 10 materials we studied, except for A. selengensis (HY) from Yueyang, Hunan, which clustered into a small branch with A. argyi, A. montana, and A. stolonifera, the remainder of A. selengensis formed a minor branch on its own, then merged with other Artemisia species to create a monophyletic group that is sister to the genus Chrysanthemum.

By extracting and comparing the non-coding regions of the complete chloroplast genomes, we conducted phylogenetic analyses using the maximum likelihood method on ten samples of A. selengensis and 27 other Asteraceae plants. The optimal model was identified as TVM + F + R2. The phylogenetic tree demonstrated well-supported branches (Fig. 13). Furthermore, it was observed that phylogenetic trees constructed from homologous protein-coding sequences and non-coding regions in the complete chloroplast genome sequences exhibited highly similar topologies and support rates.

Fig. 12
figure 12

Phylogenetic tree construction using maximum likelihood method based on sequences of homologous protein-coding genes from 10 A. selengensis and 27 other Asteraceae

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Fig. 13
figure 13

Phylogenetic tree construction using maximum likelihood method based on sequences of non-coding regions from 10 A. selengensis and 27 other Asteraceae

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Discussion

In this study, we compared the chloroplast genome sequences of 10 A. selengensis materials from six provinces, which were very similar in terms of genome size, gene number, gene sequence, and GC content, and also similar to the chloroplast genome GC content of other Artemisia plants in the Asteraceae family, such as A. annua [26]. All chloroplast genomes were relatively uniform in length, ranging from 151,148 to 151,257 bp. All genomes encoded 133 genes, including 88 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. GC content was highly conserved (37.5%), however, there were significant differences in GC content in different regions of the chloroplast genome, with the IR region having significantly higher GC content than the LSC and SSC regions, which may be due to four rRNA genes replicated in the IR region [48].

In addition, rRNA genes are more enriched in GC. The IR region of the chloroplast genome is more conserved than the LSC and SSC areas and plays a crucial function in maintaining the structure of the chloroplast genome and safeguarding critical genes [49, 50]. In our study, the chloroplast genome lengths of the 10 materials did not vary much, and the distribution of genes in the border regions was very similar with no significant changes. This indicates that the chloroplast genome of A. selengensis is highly conserved, consistent with the slow evolution of chloroplast genomes in other land plants [51].

Contraction and expansion of IR regions have an impact on the length and number of genes in the chloroplast genome of a species, leading to gene duplication, deletion, and pseudogene formation [52]. Comparative analysis of boundary regions can help in species’ phylogenetic and evolutionary analysis [53]. In this study, boundary analysis was performed on 10 A. selengensis chloroplast genomes, and it was found that the number and order of genes at the regional boundaries were highly conserved, and only the genes at the boundary junctions differed in their proximity to the boundary. Among them, rps19 and ycf1 were located at the boundaries of LSC/IRB and IRB/SSC respectively, while an overlapping region between ycf1 and ndhF was found. In contrast, gene overlap between ycf1 and ndhF was also found in A. capillaris [54] and C. humilis [55], which may be related to the contraction and expansion of the IR region.

Codons are key transmitters of genetic information and are used in the translation and synthesis of proteins from nucleic acids [56]. Also, codon use bias affects the quantity of gene expression, which is crucial for sustaining the life activities of the species, as well as the production of functional proteins [57] and also has an impact on the amount of gene expression, which is significant for maintaining the life activities of the species. In the present study, the codon usage bias of the 10 A. selengensis materials was essentially the same. The most used amino acids were arginine, serine, and leucine, with a preference for codons containing A and T bases, and with a preference for codons whose third bases ended in A and T. This result is consistent with the results of codon bias analysis of chloroplast genomes of other species [58,59,60]. However, other codons were found as start codons during translation, such as GTG (rps19) and ACG (psbL), which also occur in species of the family Araceae [61]. Through analysis of the GC content at the three codon positions, ENC-plot analysis, PR2-plot analysis, and neutrality plot analysis, it was observed that the overall GC content of the chloroplast genomes in ten Artemisia samples and the GC content at the three positions do not exceed 50%. Furthermore, the GC content decreases progressively from the first to the third position, with the overall A/T content being higher than G/C. In terms of codon usage, A/T is utilized more frequently, corresponding to the results of the RSCU (Relative Synonymous Codon Usage) analysis.

The type and number of repetitive sequences have a significant effect on chloroplast genome sequences, leading to differences in chloroplast genomes of different species [62]. We investigated the scattered repeats and microsatellite sequences in the chloroplast genomes of 10 A. selengensis materials, with 42–45 scattered repeats per material, most of which were positive repeats, and no complementary repeats were detected. Microsatellite repeats are randomly distributed in the chloroplast genome and are frequently used for species identification and phylogenetic analysis because they are co-dominant and highly polymorphic, making them effective markers for studying the genetics of plant populations [63, 64]. The number of SSRs we detected from each material ranged from 42 to 44, most commonly single nucleotide repeats, and most of the cpSSRs presented short polyadenines (ploy-A) or short polythymines (ploy-T) [65]. Most of the SSRs detected were distributed in the LSC region and the spacer region, in agreement with the results of the analysis of the genus Atractylodes [66]. The amount and distribution of repeated sequences in each material in this investigation were consistent, suggesting little variance and a low rate of variation across A. selengensis chloroplast genomes. These discovered repeated sequences may be employed as novel molecular markers in future genetic diversity investigations in Artemisia species.

In this study, chloroplast genome sequence alignment between 10 A. selengensis materials and Dongting Lake A. selengensis also showed high sequence identity and covariance, and some variable regions such as petN-psbM, rpl32-trnL-UAG were found in both non-coding and coding regions; by calculating nucleotide diversity, the nucleotide diversity values within a sliding window length of 600 bp ranged from 0 to 0.009, we identified eight mutational hotspot regions, including rpl32-trnL, ndhF-rpl32, ycf1, ndhF-rpl32, trnK(exon1) and accD. These mutational hotspots can be used as novel markers for subsequent phylogenetic analysis and DNA barcoding studies [67]. The role of selection pressure on protein-coding genes is also an important indicator for phylogenetic studies, in our study, accD, rps12, petB, and atpF genes evolved under the positive selection pressure of Ka/Ks > 1, but most genes had low Ka/Ks values and were affected by purifying selection, and no neutral selection was found in all genes.

The genus Artemisia, within the Asteraceae family, is comprised of roughly 400 species globally recognized for their adaptability, ecological significance, and medical value, notably Artemisia annua’s artemisinin for malaria treatment. Research on Artemisia contributes to our understanding of plant adaptability, evolution, and phylogeny, offering insights into species distribution and plant-environment interactions. Jiang [68] analyzed 71 protein-coding genes across 8 species of Artemisia and 13 species within the Asteraceae family, revealing that A. stechmanniana and A. tangutica share a close phylogenetic relationship, demonstrating a pronounced sisterhood bond. Concurrently, Jin et al. [69] utilized Bayesian inference (BI) and ML methods to construct a phylogenetic tree encompassing 38 Artemisia species. They found that the evolutionary branching of Artemisia was monophyletic, and all samples of the same species were clustered together; however, Artemisia belonging to various species and subspecies were not completely clustered together. Phylogenetic analysis based on a maximum likelihood method with 81 protein-coding sequences showed that all A. selengensis clustered together and then with other Artemisia species in the Asteraceae family to form the Artemisia monophyletic group, with Artemisia and Chrysanthemum as sister genera. This is consistent with the results of the chloroplast genome phylogenetic analysis of A. maritima and A. absinthium [70]. Phylogenetic trees constructed from alignments of non-coding region sequences showed consistent results with those based on protein-coding sequences in terms of topology and support rates. The genus Artemisia was confirmed as a monophyletic group, and identified as sister to the genus Chrysanthemum. This phenomenon may be associated with the inherent conservation of the chloroplast genome. Additionally, due to the relative stability of the chloroplast genome structure and the high collinearity of genes, both coding and non-coding regions exhibit synchronicity in their evolutionary patterns. In plant phylogenetic studies, the non-coding regions of the chloroplast genome can serve as an effective supplementary dataset. Analyzing these regions may enhance our understanding of the evolutionary dynamics of plant genomes and their adaptability to environmental changes, particularly when discerning differences among closely related species. Therefore, future research should delve into the phylogenetic potential of non-coding regions in various plant chloroplast genomes and explore how to effectively integrate data from both coding and non-coding regions to achieve a more comprehensive analysis of phylogenetic relationships.

Conclusions

In summary, in this study, we assembled and annotated the complete chloroplast genomes of 10 A. selengensis germplasm resources using Illumina high-throughput sequencing data, and performed a comparative analysis of the chloroplast genome structure, which showed that the chloroplast genome structure of A. selengensis from different regions, with little difference in gene type and number, was relatively conserved. The overlap of ycf1 and ndhF genes was identified by IR boundary analysis; the detected microsatellite (SSR) and differential hotspot areas discovered by whole genome sequence alignment analysis were beneficial for Artemisia population genetics and phylogenetic analysis. The phylogenetic analysis also clarified the evolutionary relationships among Artemisia species. This study has important implications for further studies on genetic diversity and evolutionary relationships in Asteraceae.

Data availability

The datasets generated during the current study are available in the NCBI repository, the persistent accession number of the dataset is as follows: ON931227, ON942235, ON968864, ON921081, ON968865, ON931228, ON960154, ON960153, ON942234, ON968863. At the same time, the BioProject ID of the whole genome sequencing data of A. selengensis chloroplast submitted to NCBI is PRJNA946329.

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Funding

This research is supported by Key R&D Program Funding Project in Hubei Province (2022BBA0064), Major Special Funding Program for the Construction of First Class Disciplines at Jianghan University(2023XKZ026), and Hubei Key Laboratory Open Fund Funding Project (EWPL202006).

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  1. Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Jianghan University, Wuhan, Hubei, China

    Yuhang Wang, Qingying Wei, Tianyuan Xue, Sixiao He & Changli Zeng

  2. School of Medicine, Jianghan University, Wuhan, Hubei, China

    Jiao Fang

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Yuhang Wang: Data processing, Writing manuscript. Qingying Wei: Collect materials. Tianyuan Xue: Statistical data. Sixiao He: Data sorting. Jiao Fang: Article modification. Changli Zeng: Conception and revision of the article.

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Statement

Ten A. selengensis materials were taken from Wuhan, Hubei, Qichun, Yueyang, Chenzhou, Nanjing, Anhui, Chuzhou, Shangrao, Jiangxi, and Yunnan, respectively. The samples are stored in the Engineering Research Center for the Protection, Development, and Utilization of Characteristic Biological Resources in the Han River Basin of Hubei Province, School of Life Sciences, Jianghan University. These samples were identified by Professor Zeng Changli, School of Life Sciences, Jianghan University. I confirm that all A. selengensis materials have been collected with permission and permission, and the methods of material collection and experimental research have been conducted in accordance with relevant guidelines/regulations/legislation. The collection of A. selengensis materials complies with the International Union for the Conservation of Nature’s Policy Statement on Endangered Species Research and the Convention on Trade in Endangered Species of Wild Fauna and Flora.

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Wang, Y., Wei, Q., Xue, T. et al. Comparative and phylogenetic analysis of the complete chloroplast genomes of 10 Artemisia selengensis resources based on high-throughput sequencing. BMC Genomics 25, 561 (2024). https://doi.org/10.1186/s12864-024-10455-3

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  • DOI: https://doi.org/10.1186/s12864-024-10455-3

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BMC Genomics

ISSN: 1471-2164

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