Pei-Gen Xiao

De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum

Various active components have been extracted from the root of Polygonum cuspidatum. However, the genetic basis for their activity is virtually unknown. In this study, 25600002 short reads (2.3 Gb) of P. cuspidatum root transcriptome were obtained via Illumina HiSeq 2000 sequencing. A total of 86418 unigenes were assembled de novo and annotated. Twelve, 18, 60 and 54 unigenes were respectively mapped to the mevalonic acid (MVA), methyl-D-erythritol 4-phosphate (MEP), shikimate and resveratrol biosynthesis pathways, suggesting that they are involved in the biosynthesis of pharmaceutically important anthraquinone and resveratrol. Eighteen potential UDP-glycosyltransferase unigenes were identified as the candidates most likely to be involved in the biosynthesis of glycosides of secondary metabolites. Identification of relevant genes could be important in eventually increasing the yields of the medicinally useful constituents of the P. cuspidatum root. From the previously published transcriptome data of 19 non-model plant taxa, 1127 shared orthologs were identified and characterized. This information will be very useful for future functional, phylogenetic and evolutionary studies of these plants.

Phytochemical and biological research of Fritillaria medicine resources.

The genus Fritillaria is a botanical source for various pharmaceutically active components, which have been commonly used in traditional Chinese medicine for thousands of years. Increasing interest in Fritillaria medicinal resources has led to additional discoveries of steroidal alkaloids, saponins, terpenoids, glycosides and many other compounds in various Fritillaria species, and to investigations on their chemotaxonomy, molecular phylogeny and pharmacology. In continuation of studies on Fritillaria pharmacophylogeny, the phytochemistry, chemotaxonomy, molecular biology and phylogeny of Fritillaria and their relevance to drug efficacy is reviewed. Literature searching is used to characterize the global scientific effort in the flexible technologies being applied. The interrelationship within Chinese Bei Mu species and between Chinese species, and species distributed outside of China, is clarified by the molecular phylogenetic inferences based on nuclear and chloroplast DNA sequences. The incongruence between chemotaxonomy and molecular phylogeny is revealed and discussed. It is essential to study more species for both the sustainable utilization of Fritillaria medicinal resources and for finding novel compounds with potential clinical utility. Systems biology and omics technologies will play an increasingly important role in future pharmaceutical research involving the bioactive compounds of Fritillaria.

Sequence characteristics and divergent evolution of the chloroplast psbA-trnH noncoding region in gymnosperms

ThepsbA-trnH intergenic region is among the most variable regions in the gymnosperm chloroplast genome. It is proposed as suitable for DNA barcoding studies and is useful in phylogenetics at the species level. This region consists of two parts differing in their evolutionary characteristics: 1) thepsbA 3′UTR (untranslated region) and 2) thepsbA-trnH intergenic spacer. We compared the sequence and RNA secondary structure of thepsbA 3′ UTR across gymnosperms and found consensus motifs corresponding to the stem portions of the RNA stem-loop structures and a consensus TGGATTGTTATGT box. ThepsbA-trnH spacer is highly variable in length and composition. Tandem repeats that form stem—loop structures were detected in both thepsbA 3′ UTR and the psbA-trnH spacer. The presence of promoters and stem—loop structures in the psbA-trnH spacer and high sequence variation in this region suggest that psbA and trnH in some gymnosperms are independently transcribed. Acomparison of chloroplast UTRs across gymnosperms offer clues to the identity of putative regulatory elements and information on selective constraints imposed on the chloroplast non-coding regions. The present study should inspire researchers to explore the full potential of thepsbA-trnH non-coding sequence and to further stimulate its application in a broader spectrum of studies, not limited to phylogenetics and DNA barcoding.

Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes

BackgroundSingle copy genes are common across angiosperm genomes. With the sufficiently high quality sequenced genomes, the identification of large-scale single copy genes among multiple species is possible. Although some characteristics have been reported, our study provides novel insights into single copy genes.ResultsWe identified single copy genes across 29 angiosperm genomes. A significant negative correlation was found between the number of duplicate blocks and the number of single copy genes. We found that a considerable number of single copy genes are located in organelles, showing a preference for binding and catalytic activity. The analysis of effective number of codons (Nc) illustrates that single copy genes have a stronger codon bias than non-single copy genes in eudicots. The relative high expression level of single copy genes was partially confirmed by the RNA-seq data, rather than the Codon Adaptation Index (CAI). Unlike in most other species, a strongly negatively correlation occurs between Nc and GC3 among single copy genes in grass genomes. When compared to all non-single copy genes, single copy genes indicate more conservation (as indicated by Ka and Ks values). But our alternative splicing (AS) results reveal that selective constraints are weaker in single copy genes than in low copy family genes (1–10 in-paralogs) and stronger than high copy family genes (>10 in-paralogs). Using concatenated shared single copy genes, we obtained a well-resolved phylogenetic tree. With the addition of intron sequences, the branch support is improved, but striking incongruences are also evident. Therefore, it is noteworthy that inclusion of intron sequences seems more appropriate for the phylogenetic reconstruction at lower taxonomic levels.ConclusionsOur analysis provides insight into the evolutionary characteristics of single copy genes across 29 angiosperm genomes. The results suggest that there are key differences in evolutionary constraints between single copy genes and non-single copy genes. And to some extent, these evolutionary constraints show some species-specific differences, especially between eudicots and monocots. Our preliminary evidence also suggests that the concatenated shared single copy genes are well suited for use in resolving phylogenetic relationships.

Mining chemodiversity from biodiversity： pharmacophylogeny of medicinal plants of Ranunculaceae

This paper reports a pharmacophylogenetic study of a medicinal plant family, Ranunculaceae, investigating the correlations between their phylogeny, chemical constituents, and pharmaceutical properties. Phytochemical, ethnopharmacological, and pharmacological data were integrated in the context of the systematics and molecular phylogeny of the Ranunculaceae. The chemical components of this family included several representative metabolic groups: benzylisoquinoline alkaloids, ranunculin, triterpenoid saponin, and diterpene alkaloids, among others. Ranunculin and magnoflorine were found to coexist in some genera. The pharmacophylogenetic analysis, integrated with therapeutic information, agreed with the taxonomy proposed previously, in which the family Ranunculaceae was divided into five sub-families: Ranunculoideae, Thalictroideae, Coptidoideae, Hydrastidoideae, and Glaucidioideae. It was plausible to organize the sub-family Ranunculoideae into ten tribes. The chemical constituents and therapeutic efficacy of each taxonomic group were reviewed, revealing the underlying connections between phylogeny, chemical diversity, and clinical use, which should facilitate the conservation and sustainable utilization of the pharmaceutical resources derived from the Ranunculaceae.

Rhizosphere Microbiota and Microbiome of Medicinal Plants: From Molecular Biology to Omics Approaches

Abstract The rhizosphere is a narrow region of soil that is directly influenced by roots and associated soil microorganisms. Research on rhizosphere microbes of various medicinal plants is essential for microbial ecology, applied microbiology and industrial biotechnology with regard to the sustainable utilization of Chinese medicinal resources. However, the inability of culturing most rhizosphere microorganisms (around 99%) in the laboratory obviates the research progress. In recent years, there is enormous advances in applying non-culturing techniques based on molecular biology and omics to the study of rhizosphere microbial diversity and plant-microbe interactions. DGGE, T-RFLP, ARDRA, DNA cloning and Sanger sequencing are still useful in the rhizosphere studies, while various omics tools, such as FISH, SIP, microarray, next generation sequencing (NGS), etc., evolve quickly to provide more comprehensive understanding of the rhizosphere microbiota and microbiome. Flexible applications of NGS technologies are here exemplified, e.g., amplicon sequencing, metagenomic sequencing, whole genome sequencing, and transcriptome sequencing, which address the biology and biotechnology potentials of the rhizosphere microbiome of medicinal plants. This review discusses recent findings and future challenges in the study of rhizosphere microbes, highlighting medicinal plant rhizosphere study, evolution of research methods, and innovative combinations of novel high-throughput techniques. The top-down approaches such as metagenomics and bottom-up approaches targeting individual species or strains should be integrated and combined with modeling approaches to afford a wide-ranging understanding of the microbial community as a whole.

The pattern of genetic diversity within Litsea coreana (Lauraceae) in China: an implication for conservation

Based on three chloroplast markers (psbA-trnH, trnL-trnF, and trnT-trnL), we identified eight haplotypes in 23 samples of Litsea coreana collected from seven provinces across southern and southwestern China. The Hap6 was the most widely distributed haplotype. The genetic diversity was highest in Sichuan Province and its adjacent regions. Therefore, these regions should be areas of priority for conservation of L. coreana in the future. In addition, our molecular dating analyses indicated that the uplift of the Tibetan Plateau and past climate changes accounted for the diversification of L. coreana in China. Finally, we found that the chemical components of L. coreana were significantly affected by both collection time and postharvest handling methods.

Anemone medicinal plants: ethnopharmacology, phytochemistry and biology

The Ranunculaceae genus Anemone (order Ranunculales), comprising more than 150 species, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine. Various medicinal compounds have been found in Anemone plants, especially triterpenoid saponins, some of which have shown anti-cancer activities. Some Anemone compounds and extracts display immunomodulatory, anti-inflammatory, antioxidant, and antimicrobial activities. More than 50 species have ethnopharmacological uses, which provide clues for modern drug discovery. Anemone compounds exert anticancer and other bioactivities via multiple pathways. However, a comprehensive review of the Anemone medicinal resources is lacking. We here summarize the ethnomedical knowledge and recent progress on the chemical and pharmacological diversity of Anemone medicinal plants, as well as the emerging molecular mechanisms and functions of these medicinal compounds. The phylogenetic relationships of Anemone species were reconstructed based on nuclear ITS and chloroplast markers. The molecular phylogeny is largely congruent with the morphology-based classification. Commonly used medicinal herbs are distributed in each subgenus and section, and chemical and biological studies of more unexplored taxa are warranted. Gene expression profiling and relevant “omics” platforms could reveal differential effects of phytometabolites. Genomics, transcriptomics, proteomics, and metabolomics should be highlighted in deciphering novel therapeutic mechanisms and utilities of Anemone phytometabolites.