scholarly journals Transcriptome Assembly of Asian Buffalo Leech Hirudinaria Manillensis and An Accurate Identification of Genes Involved in Anticoagulant Biosynthesis

2020 ◽  
Author(s):  
Chun-Xu Fan ◽  
Nibras Najm Abbood ◽  
Jun-Hui Lu ◽  
Le Wu ◽  
De-Long Guan ◽  
...  
Keyword(s):  
Expression Profile ◽  
High Reliability ◽  
Transcriptome Assembly ◽  
Length Distribution ◽  
Gc Content ◽  
Accurate Identification ◽  
Medicinal Value ◽  
Sequencing Quality ◽  
Functional Gene Analysis ◽  
Molecular Marker Development

Abstract Background: The Asian buffalo leech Hirudinaria manillensis is a valuable animal widely used in traditional Chinese medicine to cure blood-clotting. However, although the content of the anticoagulant genes in H. manillensis were identified, their actual expression profile remains undetermined. Herein, in this study we conducted transcriptome analysis on this species to address this subject.Results: A high qualified accurate gene expression profile of H. manillensis transcripts was obtained. By identifying genes upregulated during feeding, anticoagulant-related genes and signaling pathways were identified. The assembled Unigenes were compared in various mainstream databases, and a total of 16,682 Unigenes received annotation information. In addition, the Unigenes were evaluated in terms of length distribution, GC content, and expression level. The data showed good sequencing quality and high reliability. A total of 155 anticoagulant-related genes were found in this study, including those involved in different types of degradation of the extracellular matrix and inhibition of platelet aggregation.Conclusions：Substantial transcriptome information was obtained by transcriptome sequencing of H. manillensis. This information should help to provide a further molecular theoretical basis for functional gene analysis, genomics, genetic diversity analysis, and molecular marker development of H. manillensis and for the anticoagulation-related genes of this species and its medicinal value as an anticoagulant.

ISSR-Derived Species-Specific SCAR Marker for Rapid and Accurate Authentication of Ocimum tenuiflorum L.

Planta Medica ◽  
2017 ◽  
Vol 84 (02) ◽  
pp. 117-122 ◽  
Author(s):  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Priyanka Mishra ◽  
Kuppusamy Baskaran ◽  
Ashutosh Shukla ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
High Volume ◽  
Inter Simple Sequence Repeat ◽  
Rapid Identification ◽  
Medicinal Species ◽  
Accurate Identification ◽  
Sequence Characterized Amplified Region ◽  
Medicinal Value ◽  
Ocimum Tenuiflorum ◽  
Species Specific

Abstract Ocimum tenuiflorum has been widely used in traditional medicine and has high medicinal value. High volume trade of this potential medicinal plant species led to unscrupulous adulteration of both crude drugs as well as formulations. Morphology-based authentication is difficult in cases of incomplete or damaged samples and in dried herbal materials. In such cases, PCR-based molecular methods may aid in accurate identification. The present study aimed at developing species-specific DNA marker(s) for the authentication of O. tenuiflorum. A species-specific amplicon (279 bp) generated through an inter-simple sequence repeat marker (UBC 835) in all individuals of O. tenuiflorum was cloned, sequenced, and a primer pair was developed (designated as CIM-OT-835F/CIM-OT-835R). The newly developed sequence characterized amplified region marker was validated through PCR amplification in all available seven species of Ocimum, and its specificity for O. tenuiflorum was confirmed with the consistent generation of an amplicon of 177 bp. The developed marker can be used for accurate and rapid identification of the species for certification purposes and will be useful in quality control of medicinal preparations containing this important medicinal species.

scholarly journals Chloroplast Genome Analysis of The Famous Chinese Herbal Medicine Yizhiren (Zingiberaceae)

2021 ◽  
Author(s):  
JiaoYi Pan ◽  
Sun Shiyun ◽  
Xia Qiong ◽  
Lv Xvhan ◽  
Yang Xinxian ◽  
...  
Keyword(s):  
Herbal Medicine ◽  
Chloroplast Genome ◽  
Species Identification ◽  
Chinese Herbal Medicine ◽  
Gc Content ◽  
Single Copy ◽  
Likelihood Method ◽  
Chinese Herbal ◽  
Alpinia Oxyphylla ◽  
Medicinal Value

Abstract Background: Yizhiren is the fruit of Alpinia oxyphylla(Zingiberaceae) ,a well-known Chinese herbal medicine from China. The complete chloroplast genome of Alpinia oxyphylla was studied in this paper, which laid the foundation of the further study of genetic information and data of Alpinia oxyphylla.Methods: The complete chloroplast sequences of 19 the family Zingiberaceae species were aligned using MEGAX software.The phylogenetic tree was constructed by the Maximum-Likelihood method and edited by the Evolview online.Results: The chloroplast gene group is a typical tetragonal structure, which is formed by 161,351 base pairs. Each genome has a large single-copy region (LSC) of 87,248 bp, a small single-copy region (SSC) of 16,175 bp and a pair of inverted-repeat regions (IRs) of 28,964 bp in each. The complete nucleotide composition of chloroplast genome is: 31.5% A, 32.4% T, 18.2% C, 17.9% G, and the total GC content is 36.2%. Among them 28 exons and 15 introns. A total of 137 genes were annotated, which included 92 protein coding genes (PCGs), 37 metastatic RNA (tRNAs) and 8 ribosomal RNA (rRNAs).Conclusions: The phylogenetic ML tree shown the conclusion that Alpinia oxyphylla is closely related to Alpinia chinensis on genetic position relationship. This result is of great value to the study of biological inheritance, species identification and medicinal value. Meanwhile, it provides references for the study of biological inheritance, species identification and medicinal value.

scholarly journals STARRPeaker: uniform processing and accurate identification of STARR-seq active regions

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Donghoon Lee ◽  
Manman Shi ◽  
Jennifer Moran ◽  
Martha Wall ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Rna Secondary Structure ◽  
Negative Binomial ◽  
Gc Content ◽  
Active Regions ◽  
Negative Binomial Regression ◽  
Human Cell Lines ◽  
Accurate Identification ◽  
Genomic Libraries ◽  
Binomial Regression ◽  
Regression Framework

AbstractSTARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content. Furthermore, STARR-seq readout is confounded by RNA secondary structure and thermodynamic stability. To address these potential confounders, we developed a negative binomial regression framework for uniformly processing STARR-seq data, called STARRPeaker. Moreover, to aid our effort, we generated whole-genome STARR-seq data from the HepG2 and K562 human cell lines and applied STARRPeaker to comprehensively and unbiasedly call enhancers in them.

scholarly journals De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0120615 ◽  
Author(s):  
Mei Liang ◽  
Xiaoming Yang ◽  
Hang Li ◽  
Shiying Su ◽  
Hualin Yi ◽  
...  
Keyword(s):  
Molecular Marker ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Marker Development ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Molecular Marker Development

scholarly journals Protein length distribution is remarkably consistent across Life

2021 ◽  
Author(s):  
Yannis Nevers ◽  
Natasha Glover ◽  
Christophe Dessimoz ◽  
Odile Lecompte
Keyword(s):  
Gene Annotation ◽  
Length Distribution ◽  
Gc Content ◽  
Purifying Selection ◽  
Genomic Features ◽  
Protein Length ◽  
Open Questions ◽  
Size Number ◽  
A Genome ◽  
Living Species

AbstractIn every living species, the function of a protein depends on its organisation of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different evolutionary pressures, the protein length distribution, much like other genomic features, is expected to vary across species. Here we evaluated this diversity by comparing protein length distribution across 2,326 species (1,688 bacteria, 153 archaea and 485 eukaryotes). We found that proteins tend to be on average slightly longer in eukaryotes than in bacteria or archaea, but that the variation of length distribution across species is low, especially compared to the variation of other genomic features (genome size, number of proteins, gene length, GC content, isoelectric points of proteins). Moreover, most cases of atypical protein length distribution appear to be due to artifactual gene annotation, suggesting the actual variation of protein length distribution across species is even smaller. These results open the way for developing a genome annotation quality metric based on protein length distribution to complement conventional quality measures. Overall, our findings show that protein length distribution between living species is more consistent than previously thought, and provide evidence for a universal purifying selection on protein length, whose mechanism and fitness effect remain intriguing open questions.

scholarly journals The whole genome sequence and mRNA transcriptome of the tropical cyclopoid copepod Apocyclops royi

2018 ◽  
Author(s):  
Tue Sparholt Jørgensen ◽  
Bolette Lykke Holm Nielsen ◽  
Bent Petersen ◽  
Patrick Denis Browne ◽  
Benni Winding Hansen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Transcriptome Assembly ◽  
Gc Content ◽  
Small Subunit ◽  
Whole Genome Sequence ◽  
Coi Gene ◽  
Copepod Species ◽  
Cyclopoid Copepod ◽  
Whole Genome ◽  
Mrna Transcriptome

Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi. Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and only one other cyclopoid copepod had WGS resources available. Overall, the provided resources are the 7th copepod species to have WGS available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive, 76 Mb assembled repeats and 193Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available.

The Development and Testing of a Perinatal Tobacco, Attitudes, and Behaviors Survey (PTABS)

2021 ◽  
pp. JNM-D-20-00108
Author(s):  
Geraldine R. Britton ◽  
Rosemary Collier ◽  
Joyce M. Rhodes Keefe ◽  
Wendi F. Gallagher ◽  
Ann Feeney ◽  
...  
Keyword(s):  
High Reliability ◽  
Reliability And Validity ◽  
Total Sample ◽  
Nursing Intervention ◽  
Accurate Identification ◽  
Targeted Interventions ◽  
Attitudes And Behaviors ◽  
Urine Cotinine ◽  
Pregnant Smokers ◽  
And Behaviors

Background and PurposeAccurate assessment of tobacco use in pregnant smokers is key to effective nursing intervention. There is a lack of valid and reliable tools easily integrated into prenatal care. Therefore, the purpose of this study was to develop and test a perinatal survey, guided by the Health Promotion Model (HPM).MethodsThe survey was tested with 107 pregnant women via iPad. Urine cotinine assays and a process evaluation were conducted.ResultsReliability yielded a Cronbach's alpha of .873 for the ever-smoker sample and .835 for the total sample. Factors dovetailed with HPM constructs.ConclusionsPerinatal Tobacco, Attitudes, and Behaviors Survey (PTABS) exhibits high reliability and validity and is easily utilized. Updates need to include questions on all nicotine products and to be streamlined. With accurate identification of nicotine users nurses can provide targeted interventions early in pregnancy.

scholarly journals Comparative Transcriptome Analysis Identified Differentially Expressed Genes between Male and Female Flowers of Zanthoxylum armatum var. novemfolius

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 283 ◽  
Author(s):  
Xian Zhang ◽  
Ning Tang ◽  
Xiaomeng Liu ◽  
Jiabao Ye ◽  
Jingyi Zhang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Flower Development ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Zanthoxylum Armatum ◽  
Medicinal Value ◽  
Male Flowers

As a traditional spicy condiment, Zanthoxylum armatum var. novemfolius is of high economical and medicinal value. Despite the long history of human cultivation, the molecular mechanisms underlying flower development are still poorly understood in Z. armatum. In this study, we performed de novo transcriptome assembly and comparative analysis of female and male flowers in Z. armatum. A total of 94,771 unigenes were obtained, and 50,605 unigenes were successfully annotated against the public database. Transcriptome data showed that 20,431 annotated unigenes were differentially expressed genes. KEGG enrichment analysis revealed that the most representative pathway was plant hormone signal transduction. Among them, 41, 16, 41, 27, 95, and 40 unigenes were involved in the biosynthesis and signaling of abscisic acid, ethylene, cytokinin, gibberellin, auxin, and jasmonic acid, respectively. Transcription factors also played crucial roles in flower development, such as AGL11, PMADS2, and NAC. These results provided an important basis for characterizing the potential mechanism of flower development and enriching the knowledge of reproduction genetics in Z. armatum.

scholarly journals Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 543 ◽  
Author(s):  
Jun Li ◽  
Deng-Feng Xie ◽  
Xian-Lin Guo ◽  
Zhen-Ying Zheng ◽  
Xing-Jin He ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Relationship ◽  
Nucleotide Diversity ◽  
Population Genomics ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Bootstrap Support ◽  
Plastid Genomes ◽  
Medicinal Value ◽  
High Bootstrap

Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae.

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