Research topic: Herbgenomics facilitates biological study of TCM

Guest editor: LI Xi-Wen

Dr. LI Xi-Wen is now an associate professor of Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences. His major is pharmcogonosy and research subjects are herbal identificaiton, cultivition and quality traceability. He has so far published 145 scientific papers on internationally recognized academic journals including Molecular plant, New Phytologist and Biol Rev. Dr. LI joined the Editorial Board of many journals including CHIN MED-UK, CJNM, APSB, etc., and he awarded the Second Prize of State Scientific and Technological Progress in 2016. Up to now, He awarded 3 first Prizes in provincial and ministerial level and won
first Prize for International Contribution of Traditional Chinese Medicine.

Title: Herbgenomics facilitates biological study of TCM
[Abstract] Traditional Chinese Medicine (TCM) has been used for more than 5000 years and has attracted more and more world-wide attention because of its significant effect in prevention and treatment of diseases. However, the genetic background, the physio-ecological characteristics, and the molecular mechanisms of most herbs are poorly understood. The Human Genome Project opens the biological Era. Genomics triggered a revolution in system biology research and enabled people to have a deeper and comprehensive understanding of living organisms. With the development of high throughput sequencing technologies and bioinformatics, herbgenomics was put forward as a discipline to facilitate biological research of TCM. It aims to uncover the genetic information, find gene functions, discover regulatory networks of herbs and to elucidate their molecular mechanisms in the treatment of diseases. More and more biological studies were performed to examin the biology of traditional medicine including whole genome sequencing, adaptation, stress resistance, molecular identification and evolution. Herbgenomics will absolutely play an important role in research on modernization and internationalization of TCM.

Title: Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis
[Abstract] Salvia plebeia has been in use as traditional Chinese medicine (TCM) for more than 500 years. In this study, the complete chloroplast (cp) genome of S. plebeia was sequenced, assembled and compared to those of other five published Salvia cp genomes. It was found that the cp genome structure of S. plebeia was well conserved and had a total size of 151 062 bp. Four parameters were used to display the usage conditions of the codons of the amino acids in Salvia genus. Although the number of protein-coding genes in each species was the same, the total number of codons was different. Except for amino acids Trp and Met whose Relative Synonymous Codon Usage (RSCU) value of one condon was equal to 1, the remaining 19 amino acids had 1−3 preferred codons. The preferred codon names of each amino acid were coincident. The period size for the tandem repeats of six species ranged from 9 to 410 bp. Salvia cp genomes mainly possessed tandem repeats with a copy number less than or equal to 3. The sequence length of tandem repeats of the six species ranged from 25 to 824 bp. Highly viarable regions including four intergenic spacers and six partial genes were discovered as potential specific barcodes for Salvia species through cp genome-wide comparison. Finally, we performed phylogenetic analyses based on the complete cp genome and coding sequences respectively. These results provide information to help construct the cp genome library for Salvia, which may support studies of phylogenetics, DNA barcoding, population and transplastomics.

Title: Molecular structure and phylogenetic analyses of the complete chloroplast genomes of three original species of Pyrrosiae Folium
[Abstract] Pyrrosia petiolosa, Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium (PF) and commonly used as Chinese herbal medicines. Due to the similar morphological features of PF and its adulterants, common DNA barcodes cannot accurately distinguish PF species. Knowledge of the chloroplast (cp) genome is widely used in species identification, molecular marker and phylogenetic analyses. Herein, we determined the complete cp genomes of three original species of PF via high-throughput sequencing technologies. The three cp genomes exhibited a typical quadripartite structure with sizes ranging from 158 165 to 163 026 bp. The cp genomes of P. petiolosa and P. lingua encoded 130 genes, whilst that of P. sheareri encoded 131 genes. The complete cp genomes were compared, and five highly divergent regions of petA-psbJ, matK-rps16, ndhC-trnM, psbM-petN and psaC-ndhE were screened as potential DNA barcodes for identification of Pyrrosia genus species. The phylogenetic tree we obtained indicated that P. petiolosa and P. lingua are clustered in a single clade and, thus, share a close relationship. This study provides invaluable information for further studies on the species identification, taxonomy and phylogeny of Pyrrosia genus species.

Title: Genome-wide identification and analysis of AP2/ERF transcription factors related to camptothecin biosynthesis in Camptotheca acuminata
[Abstract] Camptotheca acuminata produces camptothecin (CPT), a monoterpene indole alkaloid (MIA) that is widely used in the treatment of lung, colorectal, cervical, and ovarian cancers. Its biosynthesis pathway has attracted significant attention, but the regulation of CPT biosynthesis by the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors (TFs) remains unclear. In this study, a systematic analysis of the AP2/ERF TFs family in C. acuminata was performed, including phylogeny, gene structure, conserved motifs, and gene expression profiles in different tissues and organs (immature bark, cotyledons, young flower, immature fruit, mature fruit, mature leaf, roots, upper stem, and lower stem) of C. acuminata. A total of 198 AP2/ERF genes were identified and divided into five relatively conserved subfamilies, including AP2 (26 genes), DREB (61 genes), ERF (92 genes), RAV (18 genes), and Soloist (one gene). The combination of gene expression patterns in different C. acuminata tissues and organs, the phylogenetic tree, the co-expression analysis with biosynthetic genes, and the analysis of promoter sequences of key enzymes genes involved in CPT biosynthesis pathways revealed that eight AP2/ERF TFs in C. acuminata might be involved in CPT synthesis regulation, which exhibit relatively high expression levels in the upper stem or immature bark. Among these, four genes (CacAP2/ERF123, CacAP2/ERF125, CacAP2/ERF126, and CacAP2/ERF127) belong to the ERF–B2 subgroup; two genes (CacAP2/ERF149 and CacAP2/ERF152) belong to the ERF–B3 subgroup; and two more genes (CacAP2/ERF095 and CacAP2/ERF096) belong to the DREB–A6 subgroup. These results provide a foundation for future functional characterization of the AP2/ERF genes to enhance the biosynthesis of CPT compounds of C. acuminata.

Title: Identification of medicinal plants within the Apocynaceae family using ITS2 and psbA-trnH barcodes
[Abstract] To ensure the safety of medications, it is vital to accurately authenticate species of the Apocynaceae family, which is rich in poisonous medicinal plants. We identified Apocynaceae species by using nuclear internal transcribed spacer 2 (ITS2) and psbA-trnH based on experimental data. The identification ability of ITS2 and psbA-trnH was assessed using specific genetic divergence, BLAST1, and neighbor-joining trees. For DNA barcoding, ITS2 and psbA-trnH regions of 122 plant samples of 31 species from 19 genera in the Apocynaceae family were amplified. The PCR amplification for ITS2 and psbA-trnH sequences was 100%. The sequencing success rates for ITS2 and psbA-trnH sequences were 81% and 61%, respectively. Additional data involved 53 sequences of the ITS2 region and 38 sequences of the psbA-trnH region were downloaded from GenBank. Moreover, the analysis showed that the inter-specific divergence of Apocynaceae species was greater than its intra-specific variations. The results indicated that, using the BLAST1 method, ITS2 showed a high identification efficiency of 97% and 100% of the samples at the species and genus levels, respectively, via BLAST1, and psbA-trnH successfully identified 95% and 100% of the samples at the species and genus levels, respectively. The barcode combination of ITS2/psbA-trnH successfully identified 98% and 100% of samples at the species and genus levels, respectively. Subsequently, the neighbor joining tree method also showed that barcode ITS2 and psbA-trnH could distinguish among the species within the Apocynaceae family. ITS2 is a core barcode and psbA-trnH is a supplementary barcode for identifying species in the Apocynaceae family. These results will help to improve DNA barcoding reference databases for herbal drugs and other herbal raw materials.

Title: Genome-wide identification of abscisic acid (ABA) receptor pyrabactin resistance 1-like protein (PYL) family members and expression analysis of PYL genes in response to different concentrations of ABA stress in Glycyrrhiza uralensis
[Abstract] As abscisic acid (ABA) receptor, the pyrabactin resistance 1-like (PYR/PYL) protein (named PYL for simplicity) plays an important part to unveil the signal transduction of ABA and its regulatory mechanisms. Glycyrrhiza uralensis, a drought-tolerant medicinal plant, is a good model for the mechanism analysis of ABA response and active compound biosynthesis. However, knowledge about PYL family in G. uralensis remains largely unknown. Here, 10 PYLs were identified in G. uralensis genome. Characterization analysis indicated that PYLs in G. uralensis (GuPYLs) are relatively conserved. Phylogenetic analysis showed that GuPYL1−3 belongs to subfamily I, GuPYL4−6 and GuPYL10 belong to subfamily II and GuPYL7−9 belongs to subfamily III. In addition, transcriptome data presented various expression levels of GuPYLs under different exogenous ABA stresses. The expression pattern of GuPYLs was verified by Quantitative real-time polymerase chain reaction (qRT-PCR). The study proved that GuPYL4, GuPYL5, GuPYL8 and GuPYL9 genes are significantly up-regulated by ABA stress and the response process is dynamic. This study paves the way for elucidating the regulation mechanism of ABA signal to secondary metabolites and improving the cultivation and quality of G. uralensis using agricultural strategies.