scholarly journals Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

2018 ◽  
Author(s):  
Guangyi Fan ◽  
Yuanyuan Fu ◽  
Binrui Yang ◽  
Minghua Liu ◽  
He Zhang ◽  
...  
Keyword(s):  
Disease Resistance ◽  
De Novo ◽  
Economic Value ◽  
Chinese Herb ◽  
Panax Notoginseng ◽  
Reference Sequence ◽  
Aerial Parts ◽  
Traditional Chinese Herb ◽  
Protein Encoding ◽  
Dammarenediol Synthase

AbstractPanax notoginseng is a traditional Chinese herb with high medicinal and economic value. There has been considerable research on the pharmacological activities of ginsenosides contained in Panax spp.; however, very little is known about the ginsenoside biosynthetic pathway. We reported the first de novo genome of 2.36 Gb of sequences from P. notoginseng with 35,451 protein-encoding genes. Compared to other plants, we found notable gene family contraction of disease-resistance genes in P. notoginseng, but notable expansion for several ATP-binding cassette (ABC) transporter subfamilies, such as the Gpdr subfamily, indicating that ABCs might be an additional mechanism for the plant to cope with biotic stress. Combining eight transcriptomes of roots and aerial parts, we identified several key genes, their transcription factor binding sites and all their family members involved in the synthesis pathway of ginsenosides in P. notoginseng, including dammarenediol synthase, CYP716 and UGT71. The complete genome analysis of P. notoginseng, the first in genus Panax, will serve as an important reference sequence for improving breeding and cultivation of this important nutraceutical and medicinal but vulnerable plant species.

scholarly journals Characterization of the complete chloroplast genome of traditional Chinese herb, Solanum japonense Nakai. (Solanaceae)

2021 ◽  
Vol 6 (1) ◽  
pp. 211-213
Author(s):  
Xiaoxia Zhang ◽  
Xiaofeng Zhang ◽  
Huan Wang ◽  
Shilong Chen ◽  
Tingfeng Cheng ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Chinese Herb ◽  
Complete Chloroplast Genome ◽  
Traditional Chinese Herb

scholarly journals The complete chloroplast genome of Isodon rubescens, a traditional Chinese herb

2021 ◽  
Vol 6 (2) ◽  
pp. 337-338
Author(s):  
Zhiyong Yue ◽  
Yan Wang ◽  
Baozhen Zhou ◽  
Hanping Wang
Keyword(s):  
Chloroplast Genome ◽  
Chinese Herb ◽  
Complete Chloroplast Genome ◽  
Traditional Chinese Herb

scholarly journals Traditional Chinese Herb Combined with Surgery versus Surgery for Varicocele Infertility: A Systematic Review and Meta-Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Rong-liang Dun ◽  
Min Yao ◽  
Long Yang ◽  
Xue-jun Cui ◽  
Jian-min Mao ◽  
...  
Keyword(s):  
Systematic Review ◽  
Meta Analysis ◽  
Chinese Herb ◽  
Chinese Herbs ◽  
Cochrane Library ◽  
Dichotomous Data ◽  
Surgery Group ◽  
Traditional Chinese Herb ◽  
The Cochrane Library

Objective. The objective of this study was to conduct a systematic review to assess the effectiveness and safety of traditional Chinese herb combined with surgery for male varicocele infertility compared to surgery.Methods. Randomized controlled trials (RCTs) data of traditional Chinese herbs combined with surgery for male varicocele fertility versus surgery were collected by searching the Cochrane Library, Embase, PubMed, and Chinese databases. The risk of bias was assessed using Cochrane Handbook. Study outcomes were presented as risk ratios (RRs) for dichotomous data.Results. Seventeen of 72 potentially relevant trials met the inclusion criteria. The methodological qualities of the RCTs were low. Compared with the surgery group, the traditional Chinese herb combined with surgery group had superiority in pregnancy rate at 3-month (RR=1.76, andP=0.008), 6-month (RR=1.58, andP=0.0005), and 2-year (RR=1.58, andP=0.0005) follow-ups. No RCT was found to describe the side effects.Conclusion. On considering the low methodological quality of RCTs, there was no enough evidence on traditional Chinese herb with surgery for male varicocele infertility, and more high-quality RCTs of large sample sizes are required.

scholarly journals RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Krisztian Buza ◽  
Bartek Wilczynski ◽  
Norbert Dojer
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Real Data ◽  
Reference Sequence ◽  
Individual Genome ◽  
Single Experiment ◽  
Sequencing Technologies ◽  
Sequencing Cost ◽  
The Individual ◽  
Assembly Software

Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used.Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge.Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

scholarly journals Contiguity: Contig adjacency graph construction and visualisation

2015 ◽  
Author(s):  
Mitchell J Sullivan ◽  
Nouri L Ben Zakour ◽  
Brian M Forde ◽  
Mitchell Stanton-Cook ◽  
Scott A Beatson
Keyword(s):  
De Novo ◽  
Reference Sequence ◽  
De Bruijn Graph ◽  
Interactive Software ◽  
Graph Exploration ◽  
Adjacency Graph ◽  
Highly Sensitive ◽  
Long Read ◽  
Genome Assemblies ◽  
Adjacency Graphs

Contiguity is an interactive software for the visualization and manipulation of de novo genome assemblies. Contiguity creates and displays information on contig adjacency which is contextualized by the simultaneous display of a comparison between assembled contigs and reference sequence. Where scaffolders allow unambiguous connections between contigs to be resolved into a single scaffold, Contiguity allows the user to create all potential scaffolds in ambiguous regions of the genome. This enables the resolution of novel sequence or structural variants from the assembly. In addition, Contiguity provides a sequencing and assembly agnostic approach for the creation of contig adjacency graphs. To maximize the number of contig adjacencies determined, Contiguity combines information from read pair mappings, sequence overlap and De Bruijn graph exploration. We demonstrate how highly sensitive graphs can be achieved using this method. Contig adjacency graphs allow the user to visualize potential arrangements of contigs in unresolvable areas of the genome. By combining adjacency information with comparative genomics, Contiguity provides an intuitive approach for exploring and improving sequence assemblies. It is also useful in guiding manual closure of long read sequence assemblies. Contiguity is an open source application, implemented using Python and the Tkinter GUI package that can run on any Unix, OSX and Windows operating system. It has been designed and optimized for bacterial assemblies. Contiguity is available at http://mjsull.github.io/Contiguity .

scholarly journals Implications of Genetic Distance to Reference and De Novo Genome Assembly for Clinical Genomics in Africans

2020 ◽  
Author(s):  
Daniel Shriner ◽  
Adebowale Adeyemo ◽  
Charles Rotimi
Keyword(s):  
Genetic Distance ◽  
De Novo ◽  
Reference Sequence ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
De Novo Genome Assembly ◽  
Single Nucleotide ◽  
Clinical Genomics ◽  
Advantages And Disadvantages ◽  
False Discovery

In clinical genomics, variant calling from short-read sequencing data typically relies on a pan-genomic, universal human reference sequence. A major limitation of this approach is that the number of reads that incorrectly map or fail to map increase as the reads diverge from the reference sequence. In the context of genome sequencing of genetically diverse Africans, we investigate the advantages and disadvantages of using a de novo assembly of the read data as the reference sequence in single sample calling. Conditional on sufficient read depth, the alignment-based and assembly-based approaches yielded comparable sensitivity and false discovery rates for single nucleotide variants when benchmarked against a gold standard call set. The alignment-based approach yielded coverage of an additional 270.8 Mb over which sensitivity was lower and the false discovery rate was higher. Although both approaches detected and missed clinically relevant variants, the assembly-based approach identified more such variants than the alignment-based approach. Of particular relevance to individuals of African descent, the assembly-based approach identified four heterozygous genotypes containing the sickle allele whereas the alignment-based approach identified no occurrences of the sickle allele. Variant annotation using dbSNP and gnomAD identified systematic biases in these databases due to underrepresentation of Africans. Using the counts of homozygous alternate genotypes from the alignment-based approach as a measure of genetic distance to the reference sequence GRCh38.p12, we found that the numbers of misassemblies, total variant sites, potentially novel single nucleotide variants (SNVs), and certain variant classes (e.g., splice acceptor variants, stop loss variants, missense variants, synonymous variants, and variants absent from gnomAD) were significantly correlated with genetic distance. In contrast, genomic coverage and other variant classes (e.g., ClinVar pathogenic or likely pathogenic variants, start loss variants, stop gain variants, splice donor variants, incomplete terminal codons, variants with CADD score ≥20) were not correlated with genetic distance. With improvement in coverage, the assembly-based approach can offer a viable alternative to the alignment-based approach, with the advantage that it can obviate the need to generate diverse human reference sequences or collections of alternate scaffolds.

scholarly journals Rituals in Traditional Chinese Medicine: Taking a Case of Infertility as an Example

2022 ◽  
pp. 9-12
Author(s):  
Jian Liang ◽  
Keyword(s):  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Medical Practice ◽  
Chinese Herb ◽  
Well Being ◽  
Close Connection ◽  
Research Topics ◽  
Whole Process ◽  
Traditional Chinese Herb ◽  
The World

Ritual is one of the most classic research topics in the field of Anthropology, and rituals have close connection with medial practice. However, the research on this topic from the experience of Traditional Chinese Medicine is limited. This paper presents the whole story that a patient suffering from infertility got cured got cured by a doctor of Traditional Chinese Medicine(TCM) and finally became a mother. With the detailed description of each medical practice, including pulse-taking, traditional Chinese herb therapy, and postpartum confinement, this paper analyzes the ritualized elements in the whole process, interprets how ritual play a role in the practice of TCM, and points out ritual’s essential significance in contributing to human’s well being and adjusting the relationships between individual and the world.

scholarly journals Cydrasil 3, a curated 16S rRNA gene reference package and web app for cyanobacterial phylogenetic placement

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Daniel Roush ◽  
Ana Giraldo-Silva ◽  
Ferran Garcia-Pichel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Web Application ◽  
De Novo ◽  
Reference Sequence ◽  
Rrna Gene ◽  
Automated Classification ◽  
Reference Tree ◽  
Phylogenetic Placement ◽  
Routine Identification

AbstractCyanobacteria are a widespread and important bacterial phylum, responsible for a significant portion of global carbon and nitrogen fixation. Unfortunately, reliable and accurate automated classification of cyanobacterial 16S rRNA gene sequences is muddled by conflicting systematic frameworks, inconsistent taxonomic definitions (including the phylum itself), and database errors. To address this, we introduce Cydrasil 3 (https://www.cydrasil.org), a curated 16S rRNA gene reference package, database, and web application designed to provide a full phylogenetic perspective for cyanobacterial systematics and routine identification. Cydrasil 3 contains over 1300 manually curated sequences longer than 1100 base pairs and can be used for phylogenetic placement or as a reference sequence set for de novo phylogenetic reconstructions. The web application (utilizing PaPaRA and EPA-ng) can place thousands of sequences into the reference tree and has detailed instructions on how to analyze results. While the Cydrasil web application offers no taxonomic assignments, it instead provides phylogenetic placement, as well as a searchable database with curation notes and metadata, and a mechanism for community feedback.

scholarly journals Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato

2013 ◽  
Author(s):  
Nicola Nadeau ◽  
Mayte Ruiz ◽  
Patricio Salazar ◽  
Brian Counterman ◽  
Jose Alejandro Medina ◽  
...  
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Reference Sequence ◽  
Colour Pattern ◽  
Adaptive Divergence ◽  
Population Divergence ◽  
Hybrid Zones ◽  
Data Alignment ◽  
Parallel Hybrid ◽  
Genomic Regions

Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on colour pattern. The co-mimetic species H. erato and H. melpomene have parallel hybrid zones where both species undergo a change from one colour pattern form to another. We use restriction associated DNA sequencing to obtain several thousand genome wide sequence markers and use these to analyse patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data; alignment to a reference genome and de novo assembly, and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ~15% divergent) related to the reference sequence. Our results confirm that the colour pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to colour pattern differences. We also use association mapping to identify previously unmapped colour pattern loci, in particular the Ro locus. Finally, we identify within our sample a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti.

scholarly journals The RIG-I Signal Pathway Mediated Panax notoginseng Saponin Anti-Inflammatory Effect in Ischemia Stroke

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Chujun Zhang ◽  
Sai Zhang ◽  
Lanxiang Wang ◽  
Soyeon Kang ◽  
Jiabao Ma ◽  
...  
Keyword(s):  
Cerebral Ischemia ◽  
Molecular Mechanisms ◽  
Chinese Herb ◽  
Inflammatory Cells ◽  
Panax Notoginseng ◽  
Artery Occlusion ◽  
Blue Staining ◽  
Bioactive Constituents ◽  
Anti Inflammatory ◽  
Cerebral Artery Occlusion

Panax notoginseng saponins (PNS), the main bioactive constituents of a traditional Chinese herb Panax notoginseng, were commonly used for ischemic stroke in China. However, the associated cellular and molecular mechanisms of PNS have not been well examined. This study aimed to decipher the underlying molecular target of PNS in the treatment of cerebral ischemia. The oxygen-glucose-deprived (OGD) model of rat brain microvascular endothelial cells (BMECs) was used in this study. The alteration of gene expression in rat BMECs after PNS treatment was measured by microarray and indicated that there were 38 signaling pathways regulated by PNS. Among them, RIG-I receptor and related signaling molecules TNF receptor-associated factor 2 (Traf2) and nuclear factor-kappa B (NF-κB) were significantly suppressed by PNS, which was verified again in OGD-induced BMECs measured by FQ-PCR and western blotting and in middle cerebral artery occlusion (MCAO) rats measured by immunohistochemistry. The levels of TNF-α, IL-8, and the downstream cytokines regulated by RIG-I receptor pathway were also decreased by PNS. Meanwhile, the neurological evaluation, hematoxylin and eosin (HE) staining, and Evans blue staining were conducted to evaluate the effect of PNS in MCAO rats. Results showed PNS significantly improved functional outcome and cerebral vascular leakage. Flow cytometry showed the number of the inflammatory cells infiltrated in brain tissue was decreased in PNS treatment. Our results identified that RIG-I signaling pathway mediated anti-inflammatory properties of PNS in cerebral ischemia, which provided the novel insights of PNS application in clinics.

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