Internal Transcribed Spacer (ITS) Region of Nuclear Ribosomal DNA as a Suitable DNA Barcode for Identification of Zanthoxylum armatum DC. from Manipur

Devi, Moirangthem Lakshmipriyari; Thorat, Sunil S.; Devi, Khomdram Khedashwori; Sharma, Kongbrailatpam Chandradev; Singh, Yumnam Dhaneshwor; Mishra, Amrita; Das, Sudripta

doi:10.1007/s12033-022-00518-9

Cited by 4 publications

(3 citation statements)

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“…The copyright holder for this preprint this version posted June 14, 2023. ; https://doi.org/10.1101/2023.06.13.544783 doi: bioRxiv preprint rDNA repeat, between the highly conserved small subunit, 5.8S, and the small and large subunits rRNA genes (Devi et al, 2022). In addition, the nuclear ribosomal DNA repeat is also available in thousands of copies in the nuclear genome, which facilitates its detection and amplification and is also a suitable target for the analysis of degraded genetic material.…”

Section: Coi Has Been the Most Used Genetic Marker In The Targeted De...mentioning

confidence: 99%

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Duarte

Simões

Costa

2023

Preprint

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Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, which are key to devising tools to efficiently single out a targeted species from an environmental sample, using carefully chosen marker regions and customized primers. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 460 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (75%), and to a less extent marine (14%) and terrestrial systems (10%). Vertebrates, in particular, fish (38%), and endangered species, have been the most focused in these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (22%), in particular, to target invasive species, and COI has been the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (73%), while eDNA metabarcoding has been rarely used to target single or few species (approx. 5%). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data from closely related species to assess both marker and primers specificity. In addition, eDNA-based assays developed for a particular species may have to be refined taking into account site-specific populations, as well as any intraspecific variation.

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Section: Coi Has Been the Most Used Genetic Marker In The Targeted De...mentioning

confidence: 99%

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Duarte

Simões

Costa

2023

Preprint

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“…The common and simple methods to address this problem are plant trait characterization and DNA barcoding molecular identification ( 15 ). DNA barcoding is a molecular technique that involves obtaining short DNA sequences from standardized regions of the genome for species identification ( 16 , 17 ). DNA barcoding regions can be detected in all tissues of plants regardless of factors such as growth, development, differentiation, or environment ( 18 ).…”

Section: Introductionmentioning

confidence: 99%

Integrated widely targeted metabolomics and network pharmacology revealed quality disparities between Guizhou and conventional producing areas of Codonopsis Radix

Zhang,

Yang

et al. 2023

Front. Nutr.

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IntroductionWith the internationalization of traditional Chinese medicine, the demand for medicinal and edible Codonopsis Radix (CR) has increased, and its medicinal resources have attracted attention. CR is a well-known traditional Chinese medicine with a long pharmaceutical and edible history. The Guizhou province in China has abundant CR resources, but in the absence of systematic studies on species identification and chemical compositions, the capacity of the capacity of the province to CR resource has not been fully utilized.MethodologyWe used plant morphology and DNA barcoding techniques to identify Luodang (LD) and Weidang (WD) species. To investigate the differences in metabolites between LD and WD, as well as three Chinese Pharmacopeia CRs, and to predict pharmacological mechanisms of action for the dominant differential metabolites, we utilized widely targeted metabolomics and network pharmacology. The results also revealed the material basis for the excellent food properties of both LD and WD.ResultsThe plant traits and DNA barcoding molecular identification results indicated that Luodang and Weidang from Guizhou were Codonopsis tangshen and Codonopsis pilosula, respectively. Widely targeted metabolomics analysis revealed that a total of 1,116 metabolites from 14 categories, including phenolic acids, lipids, flavonoids, were found in five CRs and shared 1,054 (94.4%) metabolites. LD and WD each contained 3 and 10 dominant differential metabolites, respectively, which were primarily flavonoids and amino acids. Amino acids, phenolic acids, and organic acids play important roles in their excellent food attributes. In CR, eight dominant differential metabolites were discovered for the first time, including isoorientin-7-O-(6″-feruloyl) glucoside, N-formyl-L-methionine, and cyclo (Phe-Glu), among others. Network pharmacology analyses showed that, in LD, dominant differential metabolites were closely related to anti-tumor, cardiovascular disease improvement, nervous system protection, and metabolic disease treatment, whereas in WD, they were closely related to nervous system protection and cardiovascular disease improvement.ConclusionThe species of LD and WD were included in the Chinese Pharmacopeia, and their metabolite profiles were remarkably similar to CR from traditional producing areas. Therefore, LD and WD can be used and promoted medicinally as CR, and they have potential value for new drug development. This study enriched the database of CR compounds and provided a reference for quality control, resource development, and new drug development of CR.

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“…Apple, has beneficial properties for human health as one of the frequently consumed fruits, is known as a source of micronutrients such as dietary fiber, vitamin C, monosaccharides, organic acids, minerals, phenolic compounds and phytochemical compounds (Wu et al, 2007;Özdemir et al, 2009;Gokdogan and Baran, 2017;Mignard et al, 2022). Using molecular markers representing genome level differences has further advantages over the traditional phenotypic method that they are stable and can be detected in all tissues of the plant regardless of growth, development, differentiation or environment (Agarwal et al, 2008;Devi et al, 2022). nrDNA ITS (internal transcribed spacer) includes ITS1, 5.8S and ITS2 regions of plants.…”

Section: Introductionmentioning

confidence: 99%

Sequence Analysis of nrDNA ITS Region in Paşa and Şah Apple (Malus × domestica) Genotypes

SEVİNDİK,

MURATHAN

2023

UASVMCN-AGR

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In this study, phylogenetic analysis of Şah and Paşa apple genotypes was performed using nrDNA ITS sequences. After the plant leaves were brought to the laboratory, gDNAs were obtained by genomic DNA isolation method. PCR amplification was performed using primers ITS4 and ITS5A. ITS sequences of some apple and Rosaceae species were retrieved from NCBI, bioinformatics analyzes were made with Bioedit 7.2.3, Finch TV 1.4.0 and MEGA 6.0 programs and phylogenetic trees were constructed. In the study, ITS sequence length of the Paşa apple genotype was 656 bp, and the ITS sequence length of the Şah apple genotype was 649 bp. Only in the maximum likelihood phylogenetic tree constructed using sequences of apple genotypes, Paşa and Şah apple genotypes appeared in the same clade as Malus domestica cultivar="Casciana'' and Malus domestica cultivar="Rotella''. In the phylogenetic tree generated including other species belonging to the Rosaceae family; apple genotypes Pyrus, Cotoneaster, Crataegus, Sorbus, Eriobotrya and Prunus were detected in a same clade. Overall results clearly suggested that the ITS sequences were both suitable for differentiation between the selected genera and were compatible with previous phylogenetic studies.

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Internal Transcribed Spacer (ITS) Region of Nuclear Ribosomal DNA as a Suitable DNA Barcode for Identification of Zanthoxylum armatum DC. from Manipur

Cited by 4 publications

References 33 publications

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Catch me if you can: current status and topical issues on the use of eDNA-based targeted detection of rare and endangered animal species

Integrated widely targeted metabolomics and network pharmacology revealed quality disparities between Guizhou and conventional producing areas of Codonopsis Radix

Sequence Analysis of nrDNA ITS Region in Paşa and Şah Apple (Malus × domestica) Genotypes

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