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Publications (116)
Nothapodytes nimmoniana is known to produce the highest content of the anticancer compound camptothecin (CPT) in the plant kingdom. We present the chromosome-level allotetraploid genome of N. nimmoniana , marking the first genome sequence from the order Icacinales. This 5-Gb genome encodes 92,630 genes, with subgenome B exhibiting dominant gene exp...
Camptotheca acuminata Decne., a significant natural source of the anticancer drug camptothecin (CPT), synthesizes CPT through the monoterpene indole alkaloid (MIA) pathway. In this study, we used single‐cell RNA sequencing (scRNA‐seq) to generate datasets encompassing over 60,000 cells from C. acuminata shoot apexes and leaves. After cell clusterin...
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Gynostemma pentaphyllum (Thunb.) Makino is an important producer of dammarene-type triterpenoid saponins. These saponins (gypenosides) exhibit diverse pharmacological benefits such as anticancer, antidiabetic, and immunomodulatory effects, and have major potential in the pharmaceutical and health care industries. Here, we employed single-cell RNA s...
Herba Epimedii (Epimedium) leaves are rich in prenylated flavonol glycosides (PFGs) with high medicinal value. However, the dynamics and regulatory network of PFG biosynthesis remain largely unclear. Here, we combined metabolite profiling (targeted to PFGs) and a high-temporal-resolution transcriptome to elucidate PFGs’ regulatory network in Epimed...
Camptotheca acuminata Decne., the main source of camptothecin (CPT), has received increasing attention for its remarkable antitumor activity. Many CPT derivatives are clinically used as effective anticancer agents worldwide. However, their biosynthesis mechanism remains unclear, and uncovering this pathway would greatly facilitate development of al...
Monoterpenoid indole alkaloids (MIAs) are among the most diverse specialized metabolites in plants and are of great pharmaceutical importance. We leveraged single-cell transcriptomics to explore the spatial organization of MIA metabolism in Catharanthus roseus leaves, and the transcripts of 20 MIA genes were first localized, updating the model of M...
Wolfiporia cocos (F. A. Wolf) has been praised as a food delicacy and medicine for centuries in China. Here, we present the genome and transcriptome of the Chinese strain CGMCC5.78 of W. cocos. High-confidence functional prediction was made for 9277 genes among the 10,908 total predicted gene models in the W. cocos genome. Up to 2838 differentially...
Unraveling the genetic basis of medicinal plant metabolism and developmental traits is a long-standing goal for pharmacologists and plant biologists. This paper discusses the definition of molecular genetics of medicinal plants, which is an integrative discipline with medicinal plants as the research object. This discipline focuses on the heredity...
Background:
Quantitative real-time reverse transcription PCR (qRT-PCR) requires a stable internal control to avoid misinterpretation of data or errors for gene expression normalization. However, there are still no validated reference genes for stable internal control in Poria cocos (Schw.) Wolf (Fuling). This study aims to validate the reference g...
Objective
To clone and analyze 3-hydroxy-3-methylglutaryl coenzyme-A synthase (HMGS) and 3-hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR) genes from Panax notoginseng of four-year old during the flowering period, the key genes involved in the mevalonic acid pathway for saponin biosynthesis.
Methods
The cDNA sequences of PnHMGS1 and PnHMGR2 w...
We cloned and analyzed the two genes of the 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase (HDR) gene family from Huperzia serrate. The two transcripts coding HDR, named HsHDR1 and HsHDR2, were discovered in the transcriptome dataset of H. serrate and were cloned by reverse transcription-polymerase chain reaction (RT-PCR). The physicochem...
Fritillaria unibracteata var. wabuensis is an important medicinal plant used for the treatment of cough symptoms related to the respiratory system. The chloroplast genome of F. unibracteata var. wabuensis (GenBank accession no. KF769142) was assembled using the PacBio RS platform (Pacific Biosciences, Beverly, MA) as a circle sequence with 151 009...
Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was...
Main conclusion
Twenty-nine genes related to phenolic acid biosynthesis were identified in the
Salvia miltiorrhiza
genome. Nineteen of these are described for the first time, with ten genes experimentally correlating to phenolic acid biosynthesis.
Vast stores of secondary metabolites exist in plants, many of which possess biological activities re...
The medicinal fungi, which are of great importance in traditional medicine, are facing the problems of wild resources scarcity and low concentration of bioactive compounds. Velvet family and LaeA global regulator play a vital role in secondary metabolism and developmental programs, which are found in a wide variety of fungi ranging from Chytridiomy...
Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, becau...
Catharanthus roseus is one of the most extensively investigated medicinal plants, which can produce more than 130 alkaloids, including the powerful antitumor drugs vinblastine and vincristine. Here we review the recent advances in the biosynthetic pathway of terpenoid indole alkaloids (TIAs) in C. roseus, and the identification and characterization...
Perilla (Perilla frutescens), an herbal plant belonging to the Lamiaceae family, has long been cultivated in Asia. Perilla is notable as an aroma-rich leaf vegetable and as the oilseed crop richest in omega-3 fatty acids. However, molecular analysis of this herbal plant is lacking due to insufficient genetic resources. Here, we constructed a normal...
A circular consensus sequencing ( CCS ) strategy involving single molecule, real‐time ( SMRT ) DNA sequencing technology was applied to de novo assembly and single nucleotide polymorphism ( SNP ) detection of chloroplast genomes.
Chloroplast DNA was purified from enriched chloroplasts of pooled individuals to construct a shotgun library for each sp...
Background
Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential.
Methods
RNA-seq analysis of adventitious roots...
RNA editing is a widespread, post-transcriptional molecular phenomenon that diversifies hereditary information across various organisms. However, little is known about genome-scale RNA editing in fungi. In this study, we screened for fungal RNA editing sites at the genomic level in Ganoderma lucidum, a valuable medicinal fungus. On the basis of our...
Ophiocordyceps sinensis is a highly valuable and popular medicinal fungus used as a tonic and roborant for thousands of years in traditional asian medicine. However, unsustainable harvesting practices have endangered this species and very little is known about its developmental programming, its biochemistry and genetics. To begin to address this, t...
Quantitative real-time reverse transcription PCR (qRT-PCR) is a rapid, sensitive, and reliable technique for gene expression studies. The accuracy and reliability of qRT-PCR results depend on the stability of the reference genes used for gene normalization. Therefore, a systematic process of reference gene evaluation is needed. Ganoderma lucidum is...
Transcription factors (TFs) are important regulating factors that can mediate many life processes. However, no TF genes have previously been reported in Panax quinquefolius (American ginseng), with the exception of a few expressed sequence tags. In this study, 753 unigenes (unique sequences) have been annotated in the plant transcription factor dat...
Research on medicinal model organism is one of the core technologies to promote the modernization of traditional Chinese medicine (TCM). The research progress of Salvia miltiorrhiza as medicinal model plant is summarized in this paper. The genome of S. miltiorrhiza is small and its life cycle is short, as well as this plant can be stably geneticall...
Dendrobium officinale Kimura et Migo (Orchidaceae) is a traditional Chinese medicinal plant. The stem contains an alkaloid that is the primary bioactive component. However, the details of alkaloid biosynthesis have not been effectively explored because of the limited number of expressed sequence tags (ESTs) available in GenBank. In this study, we a...
Background
Lonicera japonica Thunb. is a plant used in traditional Chinese medicine known for its anti-inflammatory, anti-oxidative, anti-carcinogenic, and antiviral pharmacological properties. The major active secondary metabolites of this plant are chlorogenic acid (CGA) and luteoloside. While the biosynthetic pathways of these metabolites are re...
The analysis of genes expression in buds and leaves respectively. A.Venn diagram of the unigenes in the buds and leaves of L. japonica. B.Functional classification of unigenes in the two L. japonica organs based on GO categories. Unique sequences were classified into three major categories: cellular components, molecular functions and biological pr...
Alignment of HCT amino acid sequence from Lonicera japonica and other species.
Trifolium pratense (ACI28534), Populus trichocarpa (XP002303858, XP002332068), Cynara cardunculus var. scolymus (AFL93686), Nicotiana tabacum (Q8GSM7), Coffea canephora (ABO77957, ABO47805, and ABO77955). Lonicera japonica (LjHCT1).
(TIF)
Summary of the 10 candidate HQT or HCT genes in L. japonica.
(DOC)
Alignment of HQT amino acid sequence from Lonicera japonica and other species.
Cynara cardunculus var. scolymus (ACJ23164, ADL62854, CAR92145, ACF37072, AFL93687, ABK79689, and AFL93686), Coffea canephora (ABO77957), Nicotiana tabacum (CAE46932), Solanum lycopersicum (NP001234850). Lonicera japonica (ACZ52689/LjHQT1, LjHQT2).
(TIF)
List of putative unigenes related to chlorogenic acid biosynthesis.
(DOC)
List of putative unigenes related to luteoloside biosynthesis.
(DOC)
Background
Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissue...
The authors reviewed the new technologies used for Panax genus research, including molecular identification technologies (especially for DNA barcoding), modern biotechnologies (e. g. the first generation and second generation sequencing technologies), and gene cloning and identification in this paper. These technologies have been successfully appli...
is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of , the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regio...
Primers used for assembly validation.
(DOC)
Genes present in the
Salvia miltiorrhiza
chloroplast genome.
(DOC)
Chloroplast genomic alignment between
Salvia miltiorrhiza
and
Boea hygrometrica
.
(TIF)
Chloroplast genomic alignment between
Salvia miltiorrhiza
and
Sesamum indicum
.
(TIF)
Comparison of homologues between the
Salvia miltiorrhiza
and
Boea hygrometrica
(
Bh
),
Olea europaea
(
Oe
) or
Sesamum indicum
(
Si
) chloroplast genomes using the percent identity of protein-coding sequences.
(DOC)
Size comparison of
Salvia miltiorrhiza
chloroplast genomic regions with three other Lamiales chloroplast genomes.
(DOC)
Average pairwise sequence distance of protein-coding genes among the 30 asterid chloroplast genomes.
(DOC)
Chloroplast genomic alignment between
Salvia miltiorrhiza
and
Olea europaea
.
(TIF)
The list of accession numbers of the chloroplast genome sequences used in this study.
(DOC)
Cytochrome P450 (CYP450) is a key element in the Ganoderma triterpenoid biosynthetic pathway. The catalytic reaction process for CYP450 requires NADPH / NADH for electron transfer. After searching the genome dataset of Ganoderma lucidum, the unique sequence encoding CYP450 and NADPH were discovered, separately. The open reading frames of GLCYP450 a...
Synthetic biology of traditional Chinese medicine (TCM) is a new and developing subject based on the research of secondary metabolite biosynthesis for nature products. The early development of synthetic biology focused on the screening and modification of parts or devices, and establishment of standardized device libraries. Panax notoginseng (Burk....
3-Hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR), the first enzyme of mavalonic acid pathway, is one of the key devices involved in ginsenoside biosynthesis based on synthetic biology approach. The open reading frame of a novel HMGR gene from Panax ginseng (PgHMGR2) was cloned and analyzed in this study. PgHMGR2-encoding protein showed 71.6%...
Traditional Chinese medicine (TCM) genomics and TCM synthetic biology are two hot fields in the TCM modernization. TCM genomics, including transcriptomics, structural genomics, genomic markers and functional genomics, aims to elucidate the biosynthetic pathways of TCM bioactive compounds and mine the related genes encoding enzymes involved in these...
3-Hydroxy-3-methylgutary coenzyme A reductase (HMGR, EC 1.1.1.34) catalyzes the NAD(P)H-dependent reduction of HMG-CoA to mevalonate, the first committed step in the isoprenoid pathway, which produces the largest group of contemporary natural products. We report the cloning and characterization of a full-length cDNA that encodes HMGR (designated as...
Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding...
Supplementary Figures S1-S14, Supplementary Tables S1-S14, Supplementary Notes 1-7, Supplementary Methods and Supplementary References.
The gene clusters predicted by antiSMASH software.
Analysis of Cluster of Ortholog in G. lucidum and other fungi.
GO categories of expressed genes supported by RNA-sequence data.
Comparison of DOs of G. lucidum with those of other fungi.
List of primers used for SNP detection and real-time PCR.
Cytochrome P450 physical gene clusters.
Transcriptional regulators in G. lucidum.
The gene clusters predicted by SMURF software.
Comparison of the Pfam protein families of G. lucidum with those of other fungi.
Comparison of the Pfam protein families of G. lucidum with those of other fungi.
Real-time PCR results of cytochrome P450s.
Detailed information on comparison of CAZy genes in G. lucidum with those in other fungi.
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. Tw...
Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species are largely unknown.
Using the 454 pyrosequ...
Major transcription factor families identified from P. notoginseng using Inter-Pro. The unique sequences from P. notoginseng with similarities to genes encoding transcription factors.
The discovery of SSR motifs in the putative triterpene saponin-biosynthetic genes. The SSR motifs were detected in the putative triterpene saponin-biosynthetic genes including AACT (acetyl-CoA acetyltransferase), HMGR (HMG-CoA reductase), SS (squalene synthase), SE (squalene epoxidase) and DS (dammarenediol-II synthase).
The P. notoginseng unique sequences involved in the biosynthesis of secondary metabolites. The number of unique sequences involved in the biosynthesis of alkaloid, brassinosteroid, caffeine, carotenoid, diterpenoid, flavone and flavonol, flavonoid, limonene and pinene, monoterpenoid, novobiocin, phenylpropanoid, streptomycin, terpenoid, tetracyclin...
The P. notoginseng unique sequences encoding putative transcription factors based on Inter-Pro searches. The 906 unique sequences of P. notoginseng containing transcription factor domains using Inter-Pro searches.
Cytochrome P450 discovery. The unique sequences from P. notoginseng with sequence similarities to cytochrome P450s.
Camptotheca acuminata is a Nyssaceae plant, often called the "happy tree", which is indigenous in Southern China. C. acuminata produces the terpenoid indole alkaloid, camptothecin (CPT), which exhibits clinical effects in various cancer treatments. Despite its importance, little is known about the transcriptome of C. acuminata and the mechanism of...
Peptide alignment between CaSCS and CrSCS. TIFF document of protein sequence alignment of CaSCS and CrSCS.
Gene discoveries for CPT biosynthesis against the Nr, Swissprot and Kegg databases. Excel document of specific information for mining genes in CPT biosynthesis.
Classification of transcripts annotated to cytochrome P450s in this library. Word document of the classification of cytochrome P450s transcripts.
Amino acid alignment between the predicted CaPGD and RsSGD. TIFF document of the comparison of CaPGD and RsSGD.
Gene Ontology analysis of the 454 sequencing library. TIFF document for the function categorization of the library against the Arabidopsis database.
Transcripts of CYP450s discovered in this dataset. Excel document of all the discovered transcripts of cytochrome P450.
Fritillaria cirrhosa D. Don is an endangered species in the Liliaceae family, the bulb of which is the
primary plant source for the Chinese traditional medicine “ Chuan-beimu ” , having activities that relieve
coughs and eliminates phlegm. The major pharmacologically active constituents of F. cirrhosa are
steroidal alkaloids. Two thousand one hundr...
Ginkgo biloba is monotypic species native to China and has old, dioecious, medicinally important characteristics. The functional genes related to these characteristics have not been effectively explored due to a limited number of expressed sequence tags (ESTs) from Ginkgo. To discover novel functional genes efficiently and to understand the develop...
Taxus species are highly valued as renewable resources for the production of Taxol. Despite the commercial and medicinal importance of Taxus, little genomic information is available for yew species, and Taxol biosynthesis still needs to be fully elucidated. In this study, 454 pyrosequencing technology was employed to produce an expressed sequence t...
Mapping of H. serrata and P. carinatus unique putative transcripts to KEGG biochemical pathways. List of the numbers of H. serrata and P. carinatus unique putative transcripts involved in metabolism, genetic information processing, environmental information processing, cellular processes, protein families, human diseases and unclassified in the 454...
Validation of the SSR-containing unique putative transcripts (including contigs and singletons) by PCR amplification and Sanger sequencing. Unique putative transcripts chosen from the H. serrata and P. carinatus 454-EST dataset, including five singletons and five contigs for each species. Successful amplifications of these sequences and detections...
Unique putative transcripts encoding putative CYP450s with sequence similarity between H. serrata and P. Carinatus. List of H. serrata contigs and singletons encoding putative CYP450s showing sequence similarity to Ph. carinatus unique putative transcripts.
Summary of the CYP subfamily in the H. serrata and P. carinatus 454-EST database. The number of unique putative transcripts encoding putative CYP450s from H. serrata and P. carinatus belonging to different subfamilies.
Transcripts related to phytohormones. Unique putative transcripts from H. serrata (Sheet 1) and P. carinatus (Sheet 2) with similarities to genes involved in the biosynthetic, catalytic, or signal transduction processes of phytohormones.
Plants of the Huperziaceae family, which comprise the two genera Huperzia and Phlegmariurus, produce various types of lycopodium alkaloids that are used to treat a number of human ailments, such as contusions, swellings and strains. Huperzine A, which belongs to the lycodine type of lycopodium alkaloids, has been used as an anti-Alzheimer's disease...
Herb Genome Program (HerbGP) includes a series of projects on whole genome sequencing (WGS) and post-genomics research of medicinal plants with unique secondary metabolism pathways or/and those of great medical and pharmaceutical importance. In this paper, we systematically discussed the strategy of HerbGP, from species selection, whole-genome sequ...
Huperzia serrata produces various types of lycopodium alkaloids, especially the huperzine A (HupA) that is a promising drug candidate for Alzheimer's disease. Despite the medicinal importance of H. serrata, little genomic or transcriptomic data are available from the public databases. A cDNA library was thus generated from RNA isolated from the lea...
Classification of the candidate glycosyltransferase genes. Word document containing the classification of the candidate glycosyltransferase genes according to the GO category.
Gene discovery for glycyrrhizin skeleton synthesis. Excel document containing the annotations of putative genes corresponding to the glycyrrhizin skeleton synthesis.
