Molecular structure and phylogenetic analysis of complete chloroplast genomes of medicinal species Paeonia lactiflora from Zhejiang Province

The Complete Mitochondrial Genome of Paeonia lactiflora Pall. (Saxifragales: Paeoniaceae): Evidence of Gene Transfer from Chloroplast to Mitochondrial Genome

Paeonia lactiflora (P. lactiflora), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate this matter, we sequenced and characterized the mitochondrial genome (mitogenome) of P. lactiflora. Similar to the chloroplast genome (cpgenome), the mitogenome of P. lactiflora extends across 181,688 base pairs (bp). Its unique quadripartite structure results from a pair of extensive inverted repeats, each measuring 25,680 bp in length. The annotated mitogenome includes 27 protein-coding genes, 37 tRNAs, 8 rRNAs, and two pseudogenes (rpl5, rpl16). Phylogenetic analysis was performed to identify phylogenetic trees consistent with Paeonia species phylogeny in the APG Ⅳ system. Moreover, a total of 12 MTPT events were identified and 32 RNA editing sites were detected during mitogenome analysis of P. lactiflora. Our research successfully compiled and annotated the mitogenome of P. lactiflora. The study provides valuable insights regarding the taxonomic classification and molecular evolution within the Paeoniaceae family.

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

BACKGROUD

Paeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution.

METHODS

In this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia.

RESULTS

Ranging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group.

CONCLUSIONS

Overall, this study's research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.

Development of Mini-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Medicinal Material Radix Paeoniae Rubra (Chishao)

Radix Paeoniae Rubra (Chishao), a typical multi-origin Chinese medicinal material, originates from the dried roots of Paeonia lactiflora or P. veitchii. The previous study suggested that these two commonly used Chishao showed variation in their chemical compositions and clinical efficacies. Therefore, accurate identification of different Chishao species was of great significance for the guide of clinical medication, and timely treatment of patients. In this study, the chloroplast genome sequences of P. lactiflora and P. veitchii were obtained by next-generation sequencing (NGS) technology, and then the hypervariable regions were selected to design two mini-barcode candidates for species identification. Combined with DNA metabarcoding technology, we performed qualitative and quantitative analysis on the artificially mixed samples of P. lactiflora and P. veitchii and evaluated the identification ability of these mini-barcode candidates. Furtherly, the mini-barcode with good performance was applied to distinguish the Chinese patent medicine "cerebral thrombosis tablets" containing Chishao. The results indicated that the chloroplast genomes of P. lactiflora and P. veitchii were 152,750 and 152,527 bp, respectively. As published previously, they exhibited a typical quadripartite structure including a large single-copy region (LSC), a small single-copy region (SSC) and a pair of inverted repeat regions (IRs). The nucleotide polymorphism analysis revealed seven variable protein-coding regions as petL, psaI, psbJ, rpl16, ycf1b, psaC, and ndhF, and two mini-barcodes were developed from ycf1b and ndhF respectively. The result suggested that both two mini-barcodes performed well distinguishing P. lactiflora from P. veitchii. Besides, P. lactiflora was the only raw material of Chishao in all collected "cerebral thrombosis tablets" samples. In general, this study has established a method to realize the qualitative and quantitative identification of Chishao as multi-origin Chinese medicinal materials, which can be applied to Chinese patent medicines containing Chishao.

Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships

BACKGROUND

The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species.

RESULTS

The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy.

CONCLUSIONS

Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.

Characterization of the complete chloroplast genome of the medicinal plant Orixa japonica (Rutaceae) in Zhejiang Province and its phylogenetic analysis within family Rutaceae

Orixa japonica Thunb. is an important medicinal plant belonging to the family Rutaceae. In this study, we determined the the complete chloroplast (cp) genome of O. japonica, which was 158,525 bp in length containing one large single copy region (85,965 bp), one small single copy region (18,552 bp), and a pair of inverted repeat regions (27,004 bp each). A total of 134 genes were annotated in the cp genome, including 88 protein coding genes, 37 tRNA genes, eight rRNA genes, and one pseudo gene ycf1. According to the phylogenetic analysis, O. japonica clustered together with Casimiroa edulis with high bootstrap value, indicating a close genetic relationship with subfamily Amyridoideae.

The complete chloroplast genome of the medicinal plant Polygonum cuspidatum (Polygonaceae) and its phylogenetic implications within the subfamily Polygonoideae

Polygonum cuspidatum Siebold & Zucc. is a well-known and widely used medical plant to treat arthritis, gout and inflammation. In this study, we determined the complete chloroplast genome sequence of P. cuspidatum from Zhejiang Province. The assembled chloroplast (cp) genome was 163,183 bp in length, containing two inverted repeated (IR) regions of 30,859 bp each, a large single copy (LSC) region of 87,905 bp, and a small single copy (SSC) region of 13,560 bp. The genome encodes 131 genes, consisting of 86 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content of P. cuspidatum is 37.53%, with the highest GC content of 41.27% in the IR region. The 86 protein-coding genes encode 27,597 amino acids in total, most of which use the initiation codon ATG, except the ndhD gene which starts with ACG. The length of the tRNA genes range from 48 bp to 88 bp, with the highest GC content of 62.16% in tRNA-Arg (ACG) and tRNA-Asp (GUC). A total of 66 simple sequence repeats are identified in the cp of P. cuspidatum. Phylogenetic analysis indicated a sister relationship between P. cuspidatum and Fallopia sachalinensis, suggesting a close genetic relationship between the genera of Polygonum and Fallopia. This work provides basic genetic resources for investigating the evolutionary status and population genetics of this important medicinal species.

Characterization of the complete chloroplast genome of Oxalis corymbosa DC. (Oxalidaceae), a medicinal plant from Zhejiang Province

Oxalis corymbosa DC. is an important medicinal and edible perennial herb belonging to the wood-sorrel family Oxalidaceae. In this study, we report the complete chloroplast (cp) genome sequence of O. corymbosa. The assembled chloroplast genome was 151,351 bp in length, containing two inverted repeated (IR) regions of 24,587 bp each, a large single copy (LSC) region of 85,476 bp, and a small single copy (SSC) region of 16,701 bp. The genome encodes 128 genes, consisting of 82 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene (ycf1). The 82 protein-coding genes encode 25,751 amino acids in total, most of which use the initiation codon ATG, except rps19 and psbC genes start with GTG. The lengths of the tRNA genes range from 71 bp to 93 bp, with the highest GC content of 62.16% in tRNA-Arg (ACG). The overall GC content of O. corymbosa is 36.47%, with the highest GC content of 42.64% in IR region. In addition, a total of 74 simple sequence repeats were identified in the cp genome of O. corymbosa. Phylogenetic analysis indicated a sister relationship between O. corymbosa and O. drummondii, suggesting a close genetic relationship between the two Oxalis species. This work provides basic genetic resources for investigating the evolutionary status and population genetics diversities for this medicinal species.

Complete chloroplast genome sequence of the medicinal plant ramie (Boehmeria nivea L. gaud) and its phylogenetic relationship to other Urticaceae species

Ramie (Boehmeria nivea L. Gaud) is a traditional fiber crop and important medicinal plant belonging to the family Urticaceae. In this study, we determine the complete chloroplast genome sequence of B. nivea. The assembled chloroplast genome is 156065 bp in length and shares the conserved quadripartite structure as other cp genomes in Boehmeria. The genome contains 131 genes, including 84 protein genes, 8 rRNA genes, 37 tRNA genes and 2 pseudo genes. There are 17 duplicated genes in the IR region. The overall GC content of B. nivea is 36.33%, with the highest GC content of 42.72% in IR region. A total of 67 simple sequence repeats are identified in the cp genome of B. nivea. Phylogenetic analysis demonstrated that B. nivea clustered together with B. tomentosa, further forming a monophyletic group with the species of Debregeasia and Pipturus. This work provides basic genetic resources for developing robust markers and investigating the population genetics diversities for B. nivea.