ABSTRACT
Plantago asiatica L. is a representative individual species of Plantaginaceae, whose high reputation is owed to its edible and medicinal values. However, the phylogeny and genes of the P. asiatica chloroplast have not yet been well described. Here we report the findings of a comprehensive analysis of the P. asiatica chloroplast genome. The P. asiatica chloroplast genome is 164,992 bp, circular, and has a GC content of 37.98%. The circular genome contains 141 genes, including 8 rRNAs, 38 tRNAs, and 95 protein-coding genes. Seventy-two simple sequence repeats are detected. Comparative chloroplast genome analysis of six related species suggests that a higher similarity exists in the coding region than the non-coding region, and differences in the degree of preservation is smaller between P. asiatica and Plantago depressa than among others. Our phylogenetic analysis illustrates P. asiatica has a relatively close relationship with P. depressa, which was also divided into different clades with Plantago ovata and Plantago lagopus in the genus Plantago. This analysis of the P. asiatica chloroplast genome contributes to an improved deeply understanding of the evolutionary relationships among Plantaginaceae.
Plantago asiatica Linaeus 1753. is an annual or biennial food and herb belonging to the genus Plantago of PlantaginaceaeCitation1 (). The leaves of P. asiatica are well-known as vegetables and tea in China or even East Asia.Citation2 P. asiatica as well as Plantago depressa Willd. () are traditionally used as Plantaginis herb, while their dry seeds are known as Plantaginis semen.Citation3 P. asiatica is easily cultivated, providing rich resources at low prices. It possesses good prospects in diseases prevention and treatment. Also, modern pharmacological studies have shown that the Plantaginis herb and Plantaginis semen have cholesterol degradation, anti-inflammatory, and anti-oxidation activities and can be used to treat liver disease and obesity.Citation4–7 In particular, P. asiatica seeds extract rich in phenylethanoid glycosides, flavonoids, iridoids and alkaloids have been reported to prevent heart diseases related to cardiac hypertrophy.Citation8 Polysaccharides from P. asiatica can be exploited as functional foods attributed to their thermal, antioxidant and radical-scavenging characteristics.Citation9,Citation10 Cosmetic and health care applications have been proposed for ethanol extracts from P. asiatica.Citation11 Besides, this plant has strong tolerance to formaldehyde in the air and good formaldehyde removal ability, either.Citation12 Scholars have shed light on compounds identification and clinical functions of P. asiatica, which will contribute to maximizing its economic value.Citation13 To our knowledge, no study has yet linked P. asiatica metabolites to genes in the chloroplast genome, which can be cornerstones of digging key genes and high-quality germplasm resource.Citation14
Figure 1. (a). The whole plant of P. asiatica. (b). The flowers of P. asiatica. (c). The original plant of P. depressa. (d). The specimen of P. asiatica.
The chloroplast is a key organelle where photosynthesis occurs. Energy in the atmosphere can be converted to starch, pigments, or amino acids here, which are necessary for life activities.Citation15 Chloroplast has a relatively independent genetic system called the complete chloroplast (Cp) genome. Genome sequencing has incomparable advantages in analyzing the phylogenetic relationship and further genetic diversity or evolution.Citation16 It suits plant taxonomic and adaptive evolutionary studies, especially those involved in interspecific identification.Citation17 Functions and evolutionary trajectory of different species in the family Plantaginaceae remained controversial had different active components, leading to different pharmacological effects.Citation18,Citation19 DNA barcoding in chloroplast is increasingly popular in phylogeny analyses because of its unmatched accuracy.Citation20–22 Moreover, genes detected in the chloroplast can help determine phylogenetic relationships of species belonging to the genus Plantago.Citation23 Different types of chloroplast genes have been reported to have diverse effects on metabolite regulation. The gene ycfs can modulate tetrapyrrole metabolism and biosynthesis, and overexpression of accD can increase fatty acid content in leaves.Citation24,Citation25 Based on taxonomic studies, Plantaginaceae was regarded as one of the clades of Scrophulariaceae, while it is now formally called Plantaginaceae, although it has drastically expanded from what systematists considered it to be just a few years ago.Citation26 An ambiguous perspective always existed that whether Plantaginaceae was more closely relative to Plumbaginaceae in Caryophyllales or Scrophulariaceae in Lamiales.Citation26–29 Regrettably, little available chloroplast data was published on P. asiatica, the most representative species of Plantaginaceae. Such data could help compare similar species and describe their phylogenetic relationships.
There is a need for better Cp genome data for P. asiatica. We use Illumina technology to sequence the whole chloroplast genome of P. asiatica, reporting the overall assembly, annotation, and analysis and making comparisons to other species. It will firstly provide a comprehensive analysis that is favorable for the further development and utilization of the resources.
Results and discussions
Primary characteristics of the plantago asiatica chloroplast genome
Clean data of the Cp genome of P. asiatica from Illumina sequencing was obtained with 30,787,584 reads representing 4,618,137,600 bp. After optimizing the raw data, the effective ratio of Q20 and Q30 were 97.63% and 93.39%, respectively. The sequencing quality was considered good.
The complete Cp genome of P. asiatica has a typical circular shape, the same as most angiosperms, with a length of 164,992 bp, which consists of four distinct regions: a large single-copy (LSC) region of 82,983 bp, a small single-copy (SSC) region of 4,715 bp, and a pair of inverted repeats (IR) regions of 38, 647 bp (). The GC content can also reflect the characteristics of chloroplast genome composition. It was detected that the GC content of P. asiatica Cp genome was 37.98%, which was far lower than the AT content (62.02%). The characteristics of extreme AT richness always existed in chloroplast genomes,Citation30 consistent with the consequence of this study. The IR region sequence contains eight genes encoding rRNA, so the corresponding GC content (39.90%) is significantly higher than that of the LSC (36.63%) and SSC (30.27%) regions. The skewness of it was reported to be an instruction of DNA leading and lagging chains, replication starting, and terminal points.Citation31
Table 1. The primary characteristics of the P. asiatica chloroplast genome.
Gene classification
The chloroplast genome encodes 141 genes belonging to three categories, including 95 protein coding genes, 8 ribosomal RNA (rRNA) genes, and 38 transfer RNA (tRNA) genes (). When calculating duplicated genes in the IR region, among them, 26 genes were both in the IRa and IRb regions, including 15 protein-coding genes (ccsA, ndhA, ndhB, ndhD, ndhE, ndhG, ndhH, ndhl, psaC, rpl2, rpl23, rps12, rps15, rps7, ycf2, ycf1), four rRNA genes (rrn16, rrn23, rrn4.5, rrn5) and seven tRNA genes (trnA-UGC, trnL-CAA, trnl-GAU, trnM-CAU/trnl-CAU, trnN-GUU, trnR-ACG, trnV-GAC). The SSC region consisted of three protein-coding genes (ccsA, rpl32, ndhF) and one tRNA gene (trnL-UAG). The LSC region comprised 62 protein-coding genes and 22 tRNA genes (Supplementary Table S1).
Figure 2. Circular map of the chloroplast genome of P. asiatica. Genes drawn inside the circle are transcribed clockwise, while those outsides are transcribed counter-clockwise. Genes are color-coded to imply functional groups. The dark gray area in the inner circle corresponds to the GC content while the light gray corresponds to the AT content of the genome. The SCC, LSC, IRa and IRb regions are noted in the inner circle.
Most of the protein-coding genes in the chloroplast genome of P. asiatica consisted of one exon. A total of 15 genes (rpoC1*, rps16*, rpl2*, rpl6*, ndhA*, ndhB*, atpF*, petB*, petD*, trnA-UGC*, trnG-UCC*, trnI-GAU*, trnK-UUU*, trnL-UAA*, trnV-UAC*) contained one intron and three genes (clpP1*, ycf3*, rps12*) embodied two introns (). In the anti-clockwise direction, the region between LSC and SSC is defined as IRa, and the region from SSC to LSC is IRb. What made the difference was the expression model of the trans-spliced gene rps12 observed due to separate transcription. This was verified as a gene in P. asiatica consisting of three exons, whose first exon was located in the LSC region, far from the other two exons distributed to the IR regions. The rps12 gene ligation between exon 1 and 2 has been confirmed through complementary DNA sequencing of rps12 mRNA.Citation32 Almost all protein-coding genes started with the standard initiator codon ATG, with some exceptions. The rpoC2 and rps19 began with GTC and GTG, respectively) which has been reported in the chloroplast genome of other plants.Citation33
Table 2. The length of introns and exons in genes with introns in P. asiatica.
Most chloroplast genes may play an essential role in photosynthetic pathways and self-replication. Also, some genes possess special or undefined functions. Based on the functions these genes may perform, genes in the complete Cp genome of P. asiatica were sorted into the following types overall: (1) RNA genes; (2) Transcription and translation-related genes; (3) Photosynthesis related genes; (4) Other genes; and (5) Genes of unknown function ().
Table 3. A list of genes found in the plastid genome of P. asiatica.
The gene function annotation of P. asiatica
The functional annotations from the non-redundant (NR) database of all protein-coding genes were demonstrated (Supplementary Table S2). Among them, 68 protein-coding genes were annotated in species of Plantaginaceae. There were 64 homologous genes to Plantago media, while four to Plantago maritima. The other group of genes were homologous to those in other families such as Digitalis lanata, Cajanus cajan, and Mucuna pruriens.
Functional annotation was done using Gene Ontology (GO) terms, including molecular functions (MF), cellular components (CC), and biological processes (BP) subcategories (Supplementary Table S3). The top five GO terms of these three classes are given in . This class was overrepresented among predicted molecular functions, binding, catalytic activity, transporter activity, structural molecule activity, and translation regulator activities. Most genes were related to metabolic and cellular processes attached to BP (57 and 56, respectively), followed closely by protein-containing complex and cell part in CC (52 and 42, respectively). Several genes were also involved in localization and biological regulation, among other functions.
Figure 3. Genes functional annotation in the complete chloroplast genome of P. asiatica. (a). The GO classification of genes is based on biological processes, molecular functions, and cellular components. (b). The KEGG pathway categories corresponding to genes in P. asiatica chloroplast.
By Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation,Citation34 most genes were related to metabolism, especially energy metabolism, nucleotide metabolism, and carbohydrate metabolism (). This was an important aspect of the link between the most dominant term of metabolism in the KEGG pathways and metabolic process in the GO terms. The second group was genetic information processing, such as translation and transcription. Besides, these genes were also characterized and distributed to 15 specific pathways (Supplementary Table S4). Thirty-two genes were predicted to participate in the most recurrent term “Photosynthesis”, mainly in the chloroplast, where various metabolites were produced. Notably, the gene accD in the chloroplast of P. asiatica was related to fatty acid biosynthesis and metabolism, which had been verified to improve fatty acid content in tobacco, extend leaf longevity, and result in a two-fold increase in seed yield.Citation24 The clpP1 gene encoded serine protease, which ensures normal physiological metabolic processes by degrading and removing misfolded proteins.Citation35 The clpP disruption also induced will lead to deformed leaf development and affect the accumulation of metabolites.Citation36 Hence, further work on exploring the functions of genes in chloroplast about metabolites is of great significance in P. asiatica.
SSRs and long repeat analysis
Plant genome SSRs are well-described as microsatellites and short tandem repeats (STRs). They were widely employed for molecular genetic markers and plant typing.Citation37 A total of 72 short repeats were detected, mostly single nucleotide repeats and mainly A (51) and T (56) (Supplementary Table S5). The bulk of SSRs was located in the LSC region (n = 49), with 1, 11, and 11 SSRs in the SSC, IRa, and IRb regions, respectively (). Of these, 30 short repeat types were diverse from each other, which were comprised of five SSR types: mono-nucleotide (n = 13), dinucleotide (n = 1), trinucleotide (n = 6), tetranucleotide (n = 7), and pentanucleotide (n = 3) (). Among these SSRs, 21 SSRs were only composed of A or T bases. In the other nine simple repeats, more than half of the sequence consisted of A or T bases but rarely covered tandem G or C bases. Therefore, SSRs in the P. asiatica Cp chloroplast genome were AT-rich, following the overall AT abundance of the complete sequence of the chloroplast. This finding had been reported in other chloroplast genomes, with speculation that it may be due to A-T transformation being easier than G-C transformation.Citation38 The SSRs unevenly distributed in the P. asiatica chloroplast genome can provide a theoretical basis for developing SSR molecular markers. Moreover, we also analyzed the large repeat sequence in the chloroplast. A total of 49 long tandem repeats were identified in the P. asiatica chloroplast genome (Supplementary Table S6), with the largest percentage of 44% being distributed to the LSC region. There was no long repeat located in the SSC region, while 28% repeat sequences in IRa and IRb regions (). Long tandem repeats, unlike SSRs, were dispersed in the whole genome, with 27 forward (F) repeats and 22 palindromic (P) repeats. The long repeats ranged from 40 to 659 bp.
Figure 4. The type, number, and presence of SSRs and long repeats in the Cp genome of P. asiatica. (a) Presence of SSRs in the LSC, SSC, IRa, and IRb regions. (b) Presence of long repeats in the LSC, IRa, and IRb regions. (c) Type and number of SSRs in the Cp genome of P. asiatica.
Codon usage bias
Codon usage exerts a significant influence on shaping genome evolution. As one of the numerous factors that can decide codon usage, mutational bias has a particularly crucial role in shaping the plastome evolutionary phenomenon.Citation39 These factors have been demonstrated to influence codon usage at the mutational and translational levels, but mutational pressure is the dominant force at the level of chloroplast genomes. Other mechanisms that potentially help shape the codon use bias include strand asymmetry, which causes strand-specific bias in organelle genomes.Citation40 Because of codon degeneracy, each amino acid has one to six codons. Above all, understanding the mutational and translational bias of codon usage can help explore chloroplast evolution. The inequality of synonymous codon usage results from natural selection, mutation, and genetic drift. Relative synonymous codon usage (RSCU) and codon usage measures in P. asiatica such as Nc (number of codons) values suggesting the degree of the codon usage bias, frequency of A, T, G, and C were exhibited (Supplementary Table S7). The Nc value for each protein-coding gene ranged from 23.64 (psbI) to 58.78 (clpP1), among which Nc values for rps16, rpl36, and psbT could not be calculated because they contained no amino acids with synonymous codons. Consequently, there were 28,949 codons detected in all genes (, Supplementary Table S8). The leucine encoded by six types of codons was the most abundant amino acid in this chloroplast genome (3,220 codons, 11.12%). The second abundant was isoleucine (2,362 codons, 8.16%). However, cysteine only accounted for 1.22% of amino acids. The highest value of RSCU was UUA (1.82), and the lowest was AGC (0.315). The RSCU value of 32 codons was greater than 1.00, of which 28 codon bases ended in A or U, and the remaining four ended in G. Similar to Albizia julibrissin,Citation41 the G or C terminal codons were used more frequently than expected (RSCU value < 1). And in P. asiatica, the stop codons preferred the use of TAA.
Figure 5. RSCU histogram of P. asiatica. The blocks underneath stand for different codon encoding amino acids. The columns on the top depict the sums of RSCU values of the 20 amino acids.
Prediction of RNA editing sites
RNA editing in the plastid can contribute to regulating chloroplast development.Citation42 We predicted the 47 editing sites in 16 genes (), all of which were C to T conversions. These changes in RNA editing sites all led to the transformation of amino acids, including TCA (S) to TTA (L), GCG (A) to GTG (V), CAT (H) to TAT (Y), ACC (T) to ATC (I), TCG (S) to TTG (L), and so on. The most common change was serine (S) to leucine (L), accounting for 19 (40.42%). Amino acid conversion from hydrophilic to hydrophobic can lead to an increase in protein hydrophobicity.Citation43 RNA editing enriches the genetic information of the genome as a single gene translate to different proteins. Some genes in the chloroplast must be edited to be translated normally. The gene rpl2 in maize chloroplast can be transcribed and translated normally only after the initiation codon ACG mutating into ATG.Citation44 In our study, the ndhB gene had the largest number of editing sites, up to 16. The next gene, rpoC2, has six editing sites, followed by rpoB (n = 5), rpl20 (n = 4), matK (n = 3), ndhA (n = 3), ndhD (n = 3), rps14 (n = 3), rpoA (n = 2). Only one editing site was predicted for genes accD, atpA, ccsA, ndhG, psbE, rpl2, and rpoC1, respectively.
Table 4. The predicted RNA editing sites in P. asiatica chloroplast genome.
Comparative analysis of the chloroplast genomes
To explore the potential sequence divergence of P. asiatica, we used annotation of the model plant Arabidopsis thaliana, the far relative species Platycodon grandiflorus and three species published in the genus Plantago. We plotted the total Cp genome identities in mVISTA (). Overall, sequence divergence was low across the family Plantaginaceae plastid genomes compared to other species. Among them, P. depressa possessed the highest similarity with P. asiatica, while the distantly related species P. grandiflorus had marked differences when using the A. thaliana chloroplast genome as the external reference sequence. It is worth noting that in chloroplasts of species in the same family, Plantaginaceae and other families, the substitution rates in LSC and SSC regions were mildly higher than in the IR regions.Citation45 This phenomenon has been described in many plants, which may be because of copy correction by gene conversion or the presence of conserved rRNA genes in the IR region.Citation46
Figure 6. Comparison of the Cp genome sequences of P. asiatica, P. depressa, P. ovata, P. lagopus, P. grandiflorus, and A. thaliana generated using mVISTA. Gray arrows symbolize the position and direction of the genes. Red and blue areas indicate intergenic and genic regions, respectively. Black lines represent regions of sequence identity with P. asiatica, with a 50% identity cutoff. Dashed rectangles denote highly divergent regions when P. asiatica compared to P. depressa, P. ovata, P. lagopus, P. grandifloras, and A. thaliana.
As expected, the non-coding regions showed higher sequence divergence than coding regions.Citation47 The coding regions of the clpP1, accD, ndhD, ccsA, ycf1, and ycf2 genes were quite diverse among the species in the family Plantaginaceae. The clpP1 and ycf1 genes were also different between P. asiatica and P. depressa. It is suggested that these conserved coding genes in chloroplast can be used to trace the phylogenetic relationships among lots of eudicot plants,Citation48 P. asiatica included.
Contraction and expansion in the IR area boundaries are recognized as recurrent evolutionary processes that have led to the observed variance in chloroplast genome size.Citation49 The variation of genes situated at plastome termini and boundary shifts (IR-SC) in four junctions (JLB -LSC/IRb, JSB -IRb/SSC, JSA -SSC/IRa, and JLA -IRa/LSC) were investigated. Detailed comparisons of JLB, JSB, JSA, and JLA in P. asiatica, P. lagopus, P. depressa, P. media, P. ovata, far relative species Plumbago auriculata and A. thaliana were depicted in . Compared with A. thaliana, the ndhF gene overlapped at the JSB boundary of P. asiatica, P. lagopus, P. depressa, P. media, P. ovata, P. auriculata, while this gene was not in the same position of the A. thaliana. The junction line between SSC and IRa intersected the ycf1 or ccsA gene in the family Plantaginaceae, and the gene rps15 was observed in the JSA of P. auriculata. In the family Plantaginaceae, P. asiatica showed the largest-scale inversion of expanded IR regions among these 5 species, which may be the main cause of its largest size of Cp genome. The boundaries in four junctions of P. asiatica were similar with P. depressa and P. media but differed from P. ovata and P. lagopus. There was some degree of extension into the SSC observed in P. asiatica, which to some extent occurred in other angiosperms.Citation50The gene rpl2 extended into the IRb regions ranging from 50 bp to 73 bp except P. lagopus, whose rpl2 gene was located in LSC region. The same extension can be uncovered in the ycf1 gene. It traversed the SSC and IRa regions (LR line) of P. ovata and P. lagopus. Significantly, P. ovata and P. lagopus had smaller Cp genome size than other species because the ycf1 gene was partly relocated to the SSC region by IR contraction. Contrastingly, in P. asiatica as well as the two similar species, ycf1 gene did not extend up to the SSC region and was completely duplicated in IRs. The extensions of these genes in P. asiatica may be why this was the largest genome among these five species in the family Plantaginaceae, leading to a smaller SSC region as reported in other species.Citation50
Figure 7. Comparison of the borders of the LSC, SSC, and IR regions of P. asiatica, P. lagopus, P. depressa, P. media, P. ovata, P. auriculata and Arabidopsis thaliana.
Phylogenetic relationship analysis
Phylogenetic relationship analysis in the light of chloroplast genome is more convenient than nuclear genome in tracing plant species lineages and species identification.Citation48 To resolve the phylogenetic position of P. asiatica in the genus Plantago and determine whether it is closer to Plumbaginaceae in Caryophyllales or Scrophulariaceae in Lamiales, four typical species in Gesneriaceae, Scrophulariaceae, and Plumbaginaceae were chosen, as well as five species in Plantaginaceae. The topology of the trees constructed by two different methods [maximum likelihood (ML) and Bayesian inference (BI)] was identical, confirming the robustness of our data. The bootstraps (BP) in ML analysis were presented (). BI phylogram showing branch lengths was included in Supplementary Figure S1. In the phylogenetic tree, the species can be regarded as three clades. Clade I stood for Plumbaginaceae in Caryophyllales and occupied the basal position. It was phylogenetically distant from other families. Clade II was composed of Scrophulariaceae and Gesneriaceae, supported with 98 bootstrap BP values. Plantaginaceae was divided into Clade III, consisting of two subclades with a BP value of 100. Consequently, with strong support, it uncovered that P. asiatica is closely related to P. depressa (NC041161). P. asiatica, P. depressa, and P. media (NC028520) were members of one subclade, while P. ovata (MH205737) and P. lagopus (NC041420) were distributed to the other branch in Plantaginaceae. What followed the conclusion was that P. asiatica, P. depressa, and P. media are in the subgenera of Plantago, but P. ovata and P. lagopus are in the Psyllium subgenera.Citation51 Moreover, compared with species in Gesneriaceae and Scrophulariaceae, P. asiatica had the farthest relationship with species in Plumbaginaceae.
Figure 8. Phylogenetic tree plotting using ML method, based on aligning the completed chloroplast genome sequences of Plantago asiatica L. and 17 other representative species. The numbers above the nodes are support values with ML bootstrap values. The distance bar was implied by the ML method.
Furthermore, a DNA polymorphism analysis (Pi) was used to detect low variable sites in the chloroplast genome among 18 species, showing a phylogenetic tree of only highly conserved gene sequences (, Supplementary Table S9). The average Pi was 0.08059. Genes with high Pi values can be used as molecular markers for plant identification and phylogenetic analysis.Citation52 In particular, the clpP1 (Pi = 0.23005) and matK (Pi = 0.1536) appeared highly diverse among these species. Although the morphological and chloroplast sequence were similar between P. asiatica and P. depressa, the clpP1 and ycf1 genes were hyper-variable regions between P. asiatica and other species. On the basis of the results and the sequence divergence analysis, we proposed that the clpP1 and ycf1 genes with comparatively high sequence deviation, are good for interspecies phylogenetic analysis. Moreover, the four genes with the lowest Pi values were chosen to reveal phylogenetic roles: ndhB (0.02263), psbL (0.02637), rps12(0.02901), and rps7(0.0294). Using BI and ML methods, phylogenetic analysis was also performed with these four highly conserved genes. The ML and BI phylogenetic trees of the four genes are shown in Supplementary Figures S2–S5. The most highly conserved ndhB gene was created with the same topology consistent with the complete genomes, which enabled more inference of the relationship based on the phylogenetic studies ().Citation53 The trees generated using BI or ML methods suggested P. asiatica and P. depressa formed a single clade with high bootstrap (100%) and BI support. In addition, the position of P. asiatica and the family Plantaginaceae followed the topologies from previous phylogenetic studies within Lamiales.Citation53,Citation54 However, the comprehensive analysis of P. asiatica was not operated. And Cp genome from Scrophulariaceae was not included in the previous study. Thus, the present phylogeny verifies that Plantaginaceae is closer to Gesneriaceae and Scrophulariaceae in Lamiales than Plumbaginaceae in Caryophyllales.
Figure 9. (a). Pi values of the protein coding genes. (b). Phylogenetic tree by maximum likelihood method of ndhB gene.
Materials and methods
Plant materials
Fresh and well-grown leaves of P. asiatica were obtained from a single individual from the medicinal botanical garden of Anhui University of Chinese Medicine Anhui, China (N31°56ʹ58”; E117°23ʹ38”), followed by the identification of associate Professor Qingshan Yang from the Anhui University of Chinese Medicine. A voucher specimen of this plant was stored in the Center of Herbarium, Anhui University of Chinese Medicine, Hefei, China (AhtcmH, yxy.ahtcm.edu.cn/info/1006/6713.htm, Shi-hai Xing, [email protected], under the voucher number 20211104) (). No ethical approval/permission is required in this study. Because the material used in the study is a so normal plant that can be used as vegetable. It’s neither an endangered or protected plant nor collected in any protected land. Furthermore, there’s no relative local and national regulations or guidelines in China about collecting this plant. The sample was legally collected in accordance with guidelines provided by the authors’ institution and national or international regulations. Field studies was complied with local legislation.
DNA extraction, filtering of raw reads and genome sequencing
Leaves were snap-frozen with liquid nitrogen prior to being stored at −80°C. Total mixed genomic DNA was extracted by the CTAB method, with minor changes. DNA quality and integrity were confirmed by gel electrophoresis and Nanodrop methods. DNA libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2 × 150 paired-end (PE) configuration, and image analysis and base calling were conducted by the HiSeq control software (HCS), OLB, and GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Chloroplast genome assembly and analysis
The length of the whole chloroplast genome was predicted using KmerGenie.Citation55 Short reads were quality controlled and de novo, then assembled using velvet (version 1.2.10), followed by gaps being filled using SSPACE (version 3.0)Citation56 and GapFiller (version 1–10).Citation57,Citation58 Based on the clean data, the Cp genome of P. asiatica was assembled using NOVOPlasty 2.7.2Citation59 and auxiliary software SpadesCitation60 on all the contigs, which utilized the complete Cp sequences of P. depressa (GenBank: NC041161) as the reference genome. The assembled Cp genome sequence of P. asiatica was submitted to NCBI with GenBank OL694048.
Chloroplast gene annotation
For elucidation of these genes, an online tool of the Dual Organellar GenoMe Annotator (DOGMA) programCitation61 was initially applied to annotate the P. asiatica chloroplast genome, whose protein-coding genes identity was set to 50 and hit number to 10. It is worth noting that start and stop sites of these annotated protein-coding genes needed manual correction. Ribosome RNA was detected by aligning rRNA sequences from other chloroplast genomes to ginseng chloroplast genome sequence using BLAST with global coverage and identified ≥ 90%, and tRNA was identified by tRNAscan-SECitation62 with default parameters. A circular Cp genome map was drawn using the OGDRAW program.Citation63 Then, each divided sequence was searched against the NR database using BLASTN, GO annotation by Blast2GO, and the KEGG database for identification.
Analysis of long repeats and SSRs
The web-based REPuter programCitation64 (https://bibiserv.cebitec.uni-bielefeld.de/reputer) was employed to visualize the four repetitive sequences of the Cp genome, the forward, reverse, palindrome, and complement sequences included. As for all the repeat types, the constraints set in REPuter contributed to identifying all the 90% identical repeat sequences with a minimum repeat size of 30 bp with a hamming distance equal to 3 (i.e., the gap size between repeats had a maximum length of 3 bp). All overlapping repeats were detached from the final consequences, whose repeating sequence regions were between 1 and 5 bp and repeated no less than three times were considered as SSRs. Besides, the length of repeats ≥ 20 bp were considered as large repeat sequences. The Cp SSRs were detected by MISACitation65 with search parameters of 10 repeat units for mononucleotide SSRs, five repeat units for dinucleotide SSRs, four repeat units for trinucleotide SSRs, and three repeat units for tetra-, penta-, and hexanucleotide SSRs, respectively.
Prediction of RNA editing sites and codon usage analysis
The Prep-Cp was developed to computationally identify RNA editing sites.Citation66 For the analysis, the threshold value was set to 0.8 to ensure the accuracy of the prediction. To claim the consequences of codon usage bias, we applied the program CodonW1.4.2Citation67 to analyze the synonymous codon preference of protein-coding genes shorter than 300 bp in length. Each CDS contains initiation codon and termination codon. RSCU is a qualified frequency that synonymous with every codon was specific to encoding an amino acid.
Comparison and analysis among genomes
The complete genomes of six species were compared by mVISTA,Citation68 including A. thaliana, P. grandifloras, and four species in Plantaginaceae (P. asiatica, P. depressa, P. lagopus, and P. ovata). IRscopeCitation69 was also employed to compare the borders of four main regions in the chloroplast genomes of the six species.
Phylogenetic position analysis
To detect divergence among the genus Plantago Cp genomes and its associated species, 17 species (including P. asiatica) were downloaded from the NCBI database to study the coding region evolution. Entire chloroplast genomes were used to examine these species’ average pairwise sequence divergence. Phylogenetic analysis was done after all related sequences were first aligned using MAFFT under default parameters.Citation70 Alignments were trimmed using trimAI (v.1.2).Citation71 The BIC value was used to predict the best fitting model GTRGAMMAX to perform the ML analysis by ModelTest-NG (v.0.1.4).Citation72 The final maximum likelihood tree was constructed by RAxML (v. 7.7.8)Citation73 with 1000 rapid bootstrap, which was rooted by an outgroup of A. thaliana. In addition to this, BI was employed in MrBayes (v.3.1.2). The Markov Chain Monte Carlo (MCMC) method was run using four incrementally heated chains across 1,000,000 generations, starting from random trees and sampling 1 out of every 100 generations. Pi and sequence polymorphism of the specific 18 species were analyzed using DnaSP (v 5.10.1).Citation74
Conclusion
In this study, we generated the chloroplast genome of P. asiatica with a classical tetrameric structure of 164, 992 bp in length, including 8 rRNA, 38 tRNA, and 95 protein-coding genes. Among all genes, 28,949 codons had G or C terminals. There were 47 editing sites in 16 genes, all of which were C to T conversions. Serine (S) transformation into leucine (L) can increase protein hydrophobicity. Significantly, we detected 72 SSRs in P. asiatica that can be utilized in DNA barcoding to distinguish similar species. The P. asiatica chloroplast genome shared similar overall organization and gene contents with most chloroplast genomes, including the closest species. The phylogeny analysis showed that P. asiatica formed a sister to P. depressa. Besides, Plantaginaceae was closer to Gesneriaceae and Scrophulariaceae in Lamiales than Plumbaginaceae in Caryophyllales. Our genome comparison analysis revealed highly conserved gene sequences and several differences among Plantaginaceae species, which can assist us in further studying these evolutionary relationships. Species in the family Plantaginaceae are usually difficult to distinguish due to similarities in phenotype, while different metabolites in different plants have various effects. So, these conserved gene sequences in the chloroplast genome can be used to identify species of Plantaginaceae. Our findings not only provide new insights into chloroplast genomic and phylogenetic relationships of P. asiatica but also will assist with maximizing further development and application of this plant.
Author Contributions
Conceived, designed the study: SX, DP and JW; collected specimens and prepared samples for sequencing: JW and NY, Analysis and interpretation of the data: SX, JW, JZ, and XG; Drafted the manuscript: JW and NY; Revised and criticized the manuscript: SX and DP; All authors approved the final version and agreed to accountable for all aspects of the work.
Ethics declarations
No ethical approval/permission is required in this study.
Data availability
The data that support the findings of this study are openly available in GenBank of NCBI (https://www.ncbi.nlm.nih.gov) under the access number OL694048. The associated BioProject, SRA and Bio-Sample numbers are PRJNA797537, SRR17629686, and S SAMN25008951 respectively.
Supplemental Material
Download Zip (3.1 MB)Acknowledgments
We would like to thank Genewiz Biotechnology (Suzhou) Co. Ltd in China for chloroplast genome sequencing and bioinformatics analysis.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Supplementary material
Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592324.2022.2163345
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