Introduction

Gleditsia (honey locust) is a genus comprising 13 species of the Caesalpinioideae subfamily and Fabaceae family1. The honey locust is native to North America and Asia, and a majority of the species diversity is found in eastern Asia2. Previous investigation on plants of the Gleditsia genus showed a variety of bioactivities, including anti-tumor, anti-inflammatory, anti-hyperlipidemic, anti-allergic, and analgesic3. Therefore, plants of the Gleditsia species have been widely used for centuries in local and traditional medicine1. For example, G. japonica has long been known to be a diuretic and an expectorant4, and the medicinal value of G. sinensis is documented in various editions of the Pharmacopoeia of the People’s Republic of China, from 1965 to 20155,6. Thorns of the honey locust, known as ‘Zao Jiao Ci’, are used in traditional oriental medicine as an efficacious therapeutic agent for the treatment of carbuncle, cancers, skin diseases, and suppuration7,8. Some components of G. sinensis also constitute some patent medicines, like the Gleditsia pill and Wang Bi capsules.

Angiosperm chloroplast genomes are key organelles for photosynthesis and carbon fixation9. The chloroplast genomes are valuable resources for molecular identification and phylogenetic studies because of a series of superiorities including the compact size, less recombination, maternal inheritance, self-replication, high copy number, and moderate substitution rates10,11,12,13. Comparative analysis of the chloroplast genomes of closely related species is crucial for grasping various aspects of genome evolution, focused on the structural variations and gene losses14. However, only one chloroplast genome of the genus Gleditsia has been reported so far15, which highly limits our understanding of the evolution and phylogeny of Gleditsia.

Due to their similar morphologic characteristics, unintentional adulteration of G. sinensis and G. japonica frequently occurs in China16. The current methods for distinguishing between the two include chemical17, morphological, and microscopic techniques16. However, precise discrimination of processed material of the species is often challenging18. DNA barcoding is a molecular marker technology that can accurately and rapidly identify different species and does not require any specialized training or evaluation of obvious morphological characteristics19,20. Previous studies have used the ndhF and rpl16 gene sequences21 of 11 species of the Gleditsia genus for phylogenetic and biogeographic analysis in Gleditsia. Besides, the trnL-trnF intergenic spacer and the trnL intron22 have also been used to distinguish between five Gleditsia species. Further, some researchers sequenced psbA-trnH23 and matK24 to identify G. sinensis. However, the fruits and thorns of G. sinensis, which are used in traditional medicine and several Chinese patent medicines usually undergo varying degrees of DNA degradation during harvesting, storage, and processing. Notably, the amplification of the full-length barcode in the degraded samples is challenging25. At the same time, the common markers (438–2098 bp) could introduce serious bias in biomass estimation when applied for metabarcoding analysis of degraded DNA mixtures26. To mitigate the problem of DNA degradation and quantitative inaccuracy, numerous studies have indicated that mini-barcodes (generally ≤ 200 bp) can be used instead of the traditional full-length barcodes, as they distinguish between limited species27,28,29. Therefore, our aim is to develop a mini-barcode that can be used for the quantitative identification of G. sinensis and its counterfeit G. japonica. For seed plants, such barcodes are identified by screening the chloroplast genome, owing to its advantages stated above20,30.

In this study, we sequenced the complete chloroplast genome of G. sinensis and G. japonica, which have been less studied in previous researches. The specific aims of the present study were to: (1) obtain the complete chloroplast genomes of G. sinensis and G. japonica; (2) carry out a comparative analysis of the chloroplast genomes of these two species; (3) evaluate the monophyletic and systematic position of Gleditsia by reconstructing phylogenetic relationships of the 152 species of the Fabaceae family; (4) detect the suitable mini-barcode region for species identification of these two species; (5) validate the quantitative capacity of mini-barcode primers by meta-barcoding. Our results will provide valuable data for accurate species-level discrimination between G. sinensis and G. japonica and help preserving the quality of G. sinensis as an important Chinese medicine.

Results

Complete chloroplast genome features and organization of G. sinensis and G. japonica

As shown in Fig. 1, the two Gleditsia species displayed similar quadripartite structures, including a pair of inverted repeats in the IR regions (IR), one large single-copy (LSC) region, and one small single-copy (SSC) region. The chloroplast genome sizes of G. sinensis and G. japonica were 163,175 bp and 162,391 bp, respectively. Each chloroplast genome encoded 111 unique genes, including 77 coding sequences, 30 tRNA and 4 rRNA genes. The G + C content of the G. sinensis chloroplast genome was 35.6%, which demonstrated congruence with that of G. japonica (35.5%) (Table 1). Furthermore, infA and rpl22 genes were lost in each species because of transfer to the nucleus 31,32 (Table 2). The rps12 gene was spliced into two transcripts, with exon 1 in the LSC region and exons 2 and 3 in the IR region, which is consistent with that in the previous studies33,34. 15 genes (rpl16, rpl2, rps16, rpoC1, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnV-UAC trnL-UAA, ndhA, ndhB, petB, petD, and atpF) contained one intron, and two genes, i.e., clpP, ycf3 harbored two introns (Table 2).

Figure 1
figure 1

Gene map of the complete chloroplast genomes of the two Gleditsia species. Genes on the inside of the circle are transcribed clockwise, whereas those outside are transcribed counter-clockwise. The dark gray and light gray shading within the inner circle correspond to the percentages of G + C and A + T contents, respectively.

Full size image
Table 1 Comparison of the chloroplast genome organization of the two Gleditsia species.
Full size table
Table 2 Gene contents in the chloroplast genomes of the two Gleditsia species.
Full size table

Repeated sequence analysis

Simple sequence repeats (SSR) that are highly polymorphic at the intra-specific level could be treated as molecular markers in population genetics and evolutionary studies30,35. Besides, mononucleotide SSR markers derived from chloroplast genomes form an excellent basis for studying the female lineage of polyploid species, because of their uniparental inheritance and non-recombination during sexual reproduction36,37. In this study, a total of 93 microsatellites were identified in the chloroplast genome of G. sinensis, including 87 mononucleotide and 6 dinucleotide SSR. Meanwhile, a total of 100 SSR were detected in the whole chloroplast genome of G. japonica, comprising 96 mononucleotide, 2 trinucleotide, and 2 tetranucleotide SSR (Fig. 2A). The most abundant microsatellites were mononucleotide repeats (183), accounting for about 96.45% of the total SSR (193). Among all mononucleotides, about 99.45% were A/T (182), whereas C/G (1) only accounted for 0.55% (Fig. 2B). This result is congruent with the previous observation that chloroplast genome SSR are generally composed of A/T, and rarely C/G38. The second abundant SSR were dinucleotide repeats (8), followed by trinucleotide repeats (2), while tetranucleotide, hexanucleotide and pentanucleotide repeats were not found. Our findings suggest that mononucleotide repeats may contribute to more genetic variations than other SSR, which is consistent with previous study findings35.

Figure 2
figure 2

Analysis of repeated sequences in the two Gleditsia species. (A) The numbers of different SSR types, including mononucleotide, dinucleotide, and trinucleotide; (B) Number of different SSR repeat units. (C) Frequency of repeat sequences in the two chloroplast genomes as determined by REPuter; (D) Frequency of tandem repeat sequences by length.

Full size image

According to a previous report, the contribution of longer repeat sequences to genome rearrangement and recombination is more significant than that of shorter SSR39. In this study, dispersed repeat segments in the two Gleditsia species were analyzed by REPuter. The results revealed four types of repeated sequences (forward, reverse, palindromic, and complementary) in G. sinensis, but no complementary repeats were detected in G. japonica. Figure 2C exhibits that most of these repeats were forward and palindromic, with a length range of 30–45 bps in the two Gleditsia species. Tandem repeats in both species were 120, and the majority of these repeats were between 0 and 30 bp in length (Fig. 2D). In general, the repeats identified in this study will provide valuable information for the study of population relationships in the Gleditsia species.

Analysis of codon preference

As codon usage plays a vital role in shaping chloroplast genome evolution40, the relative synonymous codon usage frequency (RSCU) between G. sinensis and G. japonica was calculated using the protein-coding sequences in the chloroplast genomes. The protein sequences contained 26,239 and 26,249 codons, respectively, including stop codons. As shown in Fig. 3 and Supplementary Tables S1–S2, leucine was encoded by the highest number (average = 10.56% and 10.45%) of codons, while cysteine (average = 1.193% and 1.192%) was the least encoded in G. sinensis and G. japonica, respectively. In addition, most of the amino acids showed codon bias except methionine (AUG) and tryptophan (UGG) (RSCU = 1), which indicated no codon preferences. Similar to the chloroplast genomes of other higher plant40,41, nearly all codons of the two species with high RSCU values (RSCU > 1.3) showed a high A/U preference in the third codon. This codon usage pattern may be driven by a composition bias for high proportions of A/T41. Meanwhile, we found that the chloroplast genome codon usage of these two species was very similar (Fig. 3). In general, the present results revealed the relative conservation of the chloroplast genomes of G. sinensis and G. japonica.

Figure 3
figure 3

Codon contents of the 20 amino acids and stop codons in all protein-coding genes in the chloroplast genomes of the two Gleditsia species.

Full size image

RNA editing site prediction

RNA editing can participate in the post-transcriptional regulation of chloroplast genomes by nucleotide insertion, deletion, or substitution, which provides an effective way of creating transcriptional and translational diversity42,43. A total of 52 and 53 RNA editing sites were predicted in 18 chloroplast genes of G. sinensis and G. japonica, respectively (Supplementary Tables S3–S4). Among these sites, the highest frequency of amino acid conversion involved serine (S) to leucine (L), which concurs with previous investigations in the chloroplast genomes of higher plant44. As previously reported, the number of shared editing sites increases in closely related taxa45. In this study, we found that G. sinensis shared editing sites with G. japonica, indicating that RNA editing was evolutionary conserved.

Comparison of the chloroplast genome structures of the two Gleditsia species

Multiple sequence alignment of the chloroplast genomes of the two Gleditsia species was performed by mVISTA, using the annotated chloroplast genome sequence of G. japonica as reference. The result (Fig. 4) showed that the genomes of the two species are highly conserved, with some degree of divergence. Comparative analysis by MAUVE showed that the chloroplast genome structures of the two Gleditsia species were identical (Supplementary Fig. S1).

Figure 4
figure 4

Visual alignment of the chloroplast genomes of the two Gleditsia species. VISTA-based identity plot showing sequence identity among the two species, using G. japonica as reference.

Full size image

Phylogenetic analysis

Recent advances in high-throughput sequencing provide large amounts of data, which could improve phylogenetic resolution41,46. Furthermore, chloroplast genomes have proven highly reliable in inferring the phylogenetic relationships between numerous plant groups47. In this study, phylogenetic relationships in the Leguminosae family were reconstructed based on 75 protein-coding genes from 155 legume species. The phylogenetic tree was divided into six subfamilies, which accorded well with the Fabaceae classification system revised in 201748 (Fig. 5), all the nodes were moderately or highly supported. In our study, three species of the Gleditsia genus formed a monophyletic clade with strong bootstrap values. The phylogenetic position of Gleditsia is consistent with previous study reports22,48,49,50. Our data will be a useful resource for molecular phylogeny studies within Leguminosae, particularly regarding the role of G. sinensis and G. japonica in plant systematics and evolution.

Figure 5
figure 5

Phylogenetic tree reconstruction of the 155 species inferred from maximum likelihood (ML) based on 75 protein-coding genes of the complete chloroplast genomes. (A) Phylogenetic relationship of Leguminosae, the orange dots at nodes on the tree indicate bootstrap values (= 100). (B) Phylogenetic relationship of Caesalpiniaceae, numbers at nodes on the tree represent bootstrap values.

Full size image

Analysis of sequence divergences and DNA mini-barcodes

Highly variable DNA regions of chloroplast genomes could be used to distinguish between closely related species51. In this study, a total of 130 genes shared between the two Gleditsia species were used to estimate nucleotide diversity. The results showed that nucleotide variability (Pi) of the two species ranged from 0.00001 to 0.02333 (Fig. 6), with a mean of 0.00210. Meanwhile, the SSC region showed the highest levels of divergence. In this region, ycf1b exhibited remarkably higher Pi values (0.02333), and was, thus, treated as a potential marker for distinguishing between these two species. Two primer pairs were designed within ycf1b using Primer352 (Table 3), and amplicons from the two Gleditsia species were compared with other plant universal marker regions of rbcL53, and ndhF, rpl1621, trnL-trnF, trnL intron22, psbA-trnH23 and matK24 as described in previous studies. As Table 4 indicates, two short regions of ycf1b (189 bp and 134 bp, respectively) had more variable sites. This result is consistent with the previous report that ycf1 is one of the most promising chloroplast DNA barcodes for land plants54. In ginsengs (another Chinese medicinal herb), ycf1b also has 100% discriminating power for closely related species20.

Figure 6
figure 6

Nucleotide diversity (Pi) based on sliding window analysis of G. sinensis and G. japonica using 130 chloroplast genes. X-axis, the position of the midpoint of a window; Y-axis, nucleotide diversity of each window.

Full size image
Table 3 Two pairs of primers of ycf1b mini-barcodes.
Full size table
Table 4 Features of nine marker regions in these two Gleditsia species.
Full size table

Validation of the quantitative capacity of mini-barcode primers by metabarcoding

The DNA of three artificial mocks consisting of two Gleditsia species was extracted, PCR conducted using the two primer pairs described above, and the respective amplicons were submitted for high-throughput sequencing. The raw data consisted of 1,549,811 reads, of which 1,394,781 high-quality reads were retained after denoising and removal of low-quality and chimeric sequences with DADA2. Subsequently, we generated 3 (product of ZJ818F-1038R) and 5 (product of ZJ1118F-1287R) reliable amplicon sequence variants (ASV) for each amplicon, respectively. In ZJ818F-1038R, all ASVs could be identified as either G. sinensis or G. japonica. For ZJ1118F-1287R, 3 ASVs could be identified, accounting for 99.9% of the total sequences (Supplementary Tables S5–S6). As expected, both primer sets could recover species with very low abundance (1.1%). The results exhibited that the two species presented positive relationships between biomass and read counts, especially for the mini-barcode of primer ZJ818F-1038R, with significant correlations (Fig. 7). Overall, we expect that this mini-barcode can be used for the quantitative identification of the two Gleditsia species in actual production.

Figure 7
figure 7

The relationship between biomass and read counts of the products amplified by the two primer pairs (ZJ818F-1038R and ZJ1118F-1287R) in the two species. X-axis, the proportion of biomass; Y-axis, the proportion of reads.

Full size image

Evaluation of the efficiency of the mini-barcode of primers ZJ818F-1038R in identifying processed medicinal materials

PCR analysis showed that primer ZJ818F-1038R had an excellent amplification efficiency of processed medicinal herbs and Chinese patent medicine (Supplementary Fig. S2). Sanger sequencing of the amplicons from Da Zao Jiao, Zao Jiao Ci, and Wang Bi capsules identified all the three samples as G. sinensis, with similarities of 99.47%, 100%, 100%, respectively (Supplementary Table S7).

Conclusions

In this study, we assembled and characterized the complete chloroplast genomes of G. sinensis and G. japonica. The basic gene information, RNA editing sites, and codon usage patterns were revealed. A total of 93 and 100 SSR were identified in the complete chloroplast genomes of G. sinensis and G. japonica, respectively. Comparative analysis showed that the two Gleditsia species have similar chloroplast genome structures and showed an overall high degree of synteny. Also, we found that ycf1b was the most variable region among 130 genes, and could, thus, be treated as a potential DNA mini-barcode marker. Quantitative analysis based on ycf1b markers using the metabarcoding method was conducted, and the result showed that primer ZJ818F-1038R have more accurate quantitative ability. Overall, the findings of our study will shed light on the genetic evolution and species identification of G. sinensis and G. japonica.

Discussion

With the increased application of high-throughput sequencing technology, the number of characterized chloroplast genomes of angiosperms is increasing rapidly55. In this study, we found that the two newly sequenced Gleditsia species have similar quadripartite structure and gene contents to the published chloroplast genomes of other members of the Caesalpinioideae sub-family15,56,57,58. According to phylogenetic analysis results, the genus Gleditsia forms a monophyletic clade with strong bootstrap values, which is consistent with the results of previous studies22,48,49,50. The Caesalpinioideae subfamily belongs to the Fabaceae family, which is divided into three long-recognized subfamilies, Caesalpinioideae, Mimosoideae, and Papilionoideae59. However, phylogenetic analysis based on matK genes48, nuclear genes (CYC2 genes)50 and chloroplast genomes15,57 suggests that the Fabaceae family should be divided into six subfamilies: Duparquetioideae, Cercidoideae, Detarioideae, Dialioideae, Caesalpinioideae, and Papilionoideae, which is now accepted widely. In our study, 155 Fabaceae species were used to construct phylogenetic trees based on chloroplast protein-coding genes. Our result is consistent with the recent phylogenomic analyses of Fabaceae.

Compared to traditional methods, DNA barcoding can be applied to accurately identify G. sinensis and its adulterant, G. japonica. DNA barcodes refer to relatively short fragments of DNA with substantial genetic variation, which can be standardized, easily amplified, and representative55. DNA degradation frequently occurs during the production of natural medicine, which can decrease the efficiency of PCR29. According to the previous studies20,25, the usage of short DNA fragments, such as mini-barcodes, can effectively mitigate this problem. Additionally, with the advancement in high-throughput sequencing and metabarcoding, the development of mini-barcode primers is encouraged, which will, in turn, improve the efficiency of taxon discovery and identification60,61, especially in mixed samples. In the present study, metabarcoding was performed via sequencing of two mini-barcode amplicons, and quantitative assessments were conducted on three artificial communities. Taberlet et al.62 have suggested that the quantitative ability of metabarcoding remains to be tested, due to primer bias. However, the PCR product of primer ZJ818F-1038R used in this study showed highly significant correlations between read counts and biomass, thus good quantitative ability. Subsequently, the mini-barcode of primer ZJ818F-1038R was found useful for identifying processed medicinal materials acquired in markets. Although the universality of our marker has not been sufficiently tested, it can solve our main problem. We believe that this mini-barcode method will guide related quality control research on other herbal medicines and that it will be continually applied in relevant research fields.

Materials and methods

Plant material preparation and sequencing

Fresh G. sinensis and G. japonica plants were picked from the garden of Tianjin University of Traditional Chinese Medicine, Tianjin, China. The voucher samples were dried and preserved in the Tianjin State Key Laboratory of Modern Chinese Medicine. A Genomic DNA extraction Kit (Sangon Biotech Co., Ltd., Shanghai, China) was used to extract the total genomic DNA. DNA purity and quantity were evaluated using a NanoPhotometer spectrophotometer (IMPLEN, CA, USA) and a Qubit 2.0 Fluorometer (Life Technologies, CA, USA), respectively. The sequencing library was generated by a Truseq Nano DNA HT Sample Preparation Kit (Illumina USA) following the manufacturer’s recommendations. The library was sequenced on Illumina HiSeq X Ten platform, and 150 bp paired-end reads were generated.

Complete chloroplast genome construction and annotation

The total clean reads (G. sinensis and G. japonica) were filtered and assembled into contigs using GetOrganelle pipeline63. After that, the clean reads were re-mapped to the complete draft chloroplast genome to confirm each base, respectively. We used different tools such as DOGMA64, CPGAVAS265, and GeSeq66 to annotate genes of the chloroplast genome. tRNAscan-SE67 was employed to verify the tRNA genes. All genes were inspected carefully against the published complete chloroplast genomes of Caesalpiniaceae (KU569489, MF741770, NC_026134, NC_028732, NC_028733, NC_034986, NC_034987, NC_034988, NC_034989, NC_034990, NC_034991, NC_034992, NC_035346, NC_035347, and NC_035348). All the start and stop codons were adjusted manually. Subsequently, the physical maps of the two complete chloroplast genome sequences were visualized with OrganellarGenomeDRAW68. The annotated genome sequences of G. sinensis and G. japonica were submitted to the GenBank (accession numbers: MK817503, MK817502).

Repeated sequences and microsatellites

MISA69 was employed to predict single sequence repeats (SSR) or microsatellites in the complete chloroplast genome of the two Gleditsia species. The minimum number of repeats was set to 10, 6, 5, 5, 5, and 5 for mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide, respectively. We also identified forward (F), reverse (R), complementary (C), and palindromic (P) repeats using the online REPuter software70, with a minimum repeat size of 30 bp and a Hamming distance of 3. Tandem repeats were detected by Tandem Repeats Finder web tool71, using default parameters.

Analysis and comparison of genome structures

Codon usage was determined by MEGA-X72. 35 protein-coding genes of G. sinensis and G. japonica chloroplast genomes were used to predict the potential RNA editing sites by the online program Predictive RNA Editor for Plants suite73, using default parameters. The program mVISTA74 in Shuffle-LAGAN mode was used to perform the structural comparison of two chloroplast genomes. At the same time, structural variations between the two Gleditsia chloroplast genomes were further compared by the Mauve software75.

Phylogenetic analysis

Phylogenetic analysis was based on 75 shared protein-coding genes of the chloroplast genomes of 155 members of the Leguminosae family, including G. sinensis and G. japonica. Rumex acetosa (Polygonaceae) was used as an outgroup (Supplementary Table S8). Alignments were performed by MAFFT v7 with default parameters76. A maximum likelihood (ML) approach was used to infer phylogenetic relationships. Maximum likelihood analysis was performed using IQ-TREE v1.6.177, with 1,000 bootstrap replicates. The best-fit model was determined by ModelFinder78.

Analysis of sequence divergences

To analyze nucleotide diversity, we performed a sliding window analysis to assess nucleotide variability (Pi) by the DnaSP software version 6.11.0179. The window length was set to 600 bp, and the step size was 200 bp.

Validation of the quantitative capacity of mini-barcode primers by metabarcoding

To verify the quantitative ability of these two primer pairs in our subjects, three mock communities were prepared, containing G. sinensis and G. japonica (Supplementary Table S9). Genomic DNA was extracted from each mock community, respectively. The target regions were amplified using two pairs of fusion primers with matching tags (e.g., F1-R1, F2-R2.) (Supplementary Table S10) to ensure that tag jumps would not result in the false assignment of sequences to samples80. PCR amplification was conducted in a 25 μl reaction composed of 12.5 μl of TaKaRa 2 × Gflex PCR Buffer (containing 1 mM of Mg2+ and 200 μM of each dNTP), 0.2 μM of each primer, 0.5 μl Tks Gflex DNA Polymerase (1.25 units/μl), approximately 10 μl ddH2O, and 30–50 ng DNA. The PCR protocol was as follows: preheating at 94 °C for 1 min, 30 cycles at 98 °C for 10 s, annealing at 55 °C for 15 s, and elongation at 68 °C for 30 s, followed by a final extension at 68 °C for 5 min. Negative controls were included in each run. Amplicons (including negative controls) were resolved on 1.5% agarose gels and sequenced (2 × 150 bp paired‐ends) on the Illumina Hiseq X Ten platform.

The fastq-multx81,82 was used to split data according to the tag sequences. Primer sequences were trimmed by BBDuk (https://sourceforge.net/projects/bbmap/). To construct ASV, denoise, and quality control (including removal of chimeras) were performed with the DADA283. Meanwhile, reads were truncated to exclude low-quality data (N120 bp for forward reads and N120 bp for reverse reads, truncQ = 2, maxEE = 2). In addition, taxonomy was assigned to ASV with the chloroplast genome in our work (99% similarity at least). The relationship between biomass and individual reads was visualized for each species.

Evaluation of the efficiency of the mini-barcode of primers ZJ818F-1038R in identifying processed medicinal materials

Two samples from different parts of G. sinensis, named Da Zao Jiao (fruit), Zao Jiao Ci (thorn), and one type of Chinese patent medicine (Wang Bi capsules), were purchased from the market to test the amplification ability of primers ZJ818F-1038R. PCR method was similar to the part of “Validation the quantitative capacity of mini-barcode primers by metabarcoding”. PCR products were sequenced by the Sanger method.