Application of InDel markers based on the chloroplast genome sequences for authentication and traceability of tartary and common buckwheat

A reliable, qualitative PCR-based detection method for the traceability and authentication of common and Tartary buckwheat was developed. Five InDel markers developed from chloroplast genome variation between the two species were applied for 96 buckwheat accessions and all accessions were easily differentiated as Tartary and common buckwheat using these markers. We also determined the sample detection limit by PCR and qPCR as 0.001 and 0.02 ng/µl, respectively. InDel markers could detect the mixture of two species flour up to 10% contamination. InDel markers were also applied to processed foods such as noodles and tea, and we found that species-specific PCR bands could be used to identify buckwheat even after processing. Hence, these InDel markers are simple with higher specificity and sensitivity and are reliable for the authentication of buckwheat processed foods.

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Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP

Planta Medica ◽

10.1055/s-0043-113449 ◽

2017 ◽

Vol 83 (18) ◽

pp. 1420-1430 ◽

Cited By ~ 12

Author(s):

Ning Zhang ◽

Padmini Ramachandran ◽

Jun Wen ◽

James Duke ◽

Helen Metzman ◽

...

Keyword(s):

Dietary Supplements ◽

Chloroplast Genome ◽

Related Species ◽

Sequencing Data ◽

Genome Sequences ◽

Closely Related Species ◽

Chloroplast Genomes ◽

Processed Products ◽

Species Specific ◽

Close Relatives

AbstractPrecise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences. Here, we introduce a repository of complete chloroplast genome sequences called GenomeTrakrCP, which will be publicly available at the National Center for Biotechnology Information (NCBI). Target species for inclusion are plants found in foods and dietary supplements, toxin producers, common contaminants and adulterants, and their close relatives. Publicly available data will include annotated assemblies, raw sequencing data, and voucher information with each NCBI accession associated with an authenticated reference herbarium specimen. To date, 40 complete chloroplast genomes have been deposited in GenomeTrakrCP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA325670/), and this will be expanded in the future.

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Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences

The Plant Pathology Journal ◽

10.5423/ppj.oa.04.2015.0049 ◽

2015 ◽

Vol 31 (3) ◽

pp. 212-218 ◽

Cited By ~ 1

Author(s):

Chang-Gi Back ◽

Seung-Yeol Lee ◽

Boo-Ja Lee ◽

Mi-Chi Yea ◽

Sang-Mok Kim ◽

...

Keyword(s):

Genome Sequences ◽

Pcr Assay ◽

Specific Pcr ◽

Xanthomonas Species ◽

Specific Pcr Assay ◽

Species Specific

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A species-specific PCR forLactobacillus inersdemonstrates a relative specificity of this species for vaginal colonization

Microbial Ecology in Health and Disease ◽

10.3402/mehd.v20i3.7589 ◽

2008 ◽

Vol 20 (3) ◽

Author(s):

Mohammed A. Alqumber ◽

Jeremy P. Burton ◽

Celia Devenish ◽

John R. Tagg

Keyword(s):

Specific Pcr ◽

Vaginal Colonization ◽

Relative Specificity ◽

Species Specific

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Survey on Perkinsus Species in Manila Clam Ruditapes philippinarum in Korean Waters Using Species-Specific PCR

Fish Pathology ◽

10.3147/jsfp.52.202 ◽

2017 ◽

Vol 52 (4) ◽

pp. 202-205 ◽

Cited By ~ 3

Author(s):

Hyun-Sil Kang ◽

Hyun-Sung Yang ◽

Kimberly S. Reece ◽

Young-Ghan Cho ◽

Hye-Mi Lee ◽

...

Keyword(s):

Ruditapes Philippinarum ◽

Manila Clam ◽

Korean Waters ◽

Specific Pcr ◽

Species Specific

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The complete chloroplast genome sequences of five Miscanthus species, and comparative analyses with other grass plastomes

Industrial Crops and Products ◽

10.1016/j.indcrop.2021.113248 ◽

2021 ◽

Vol 162 ◽

pp. 113248

Author(s):

Jiajing Sheng ◽

Mi Yan ◽

Jia Wang ◽

Lingling Zhao ◽

Fasong Zhou ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Comparative Analyses

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Development of a Co-Dominant Cleaved Amplified Polymorphic Sequences Assay for the Rapid Detection and Differentiation of Two Pathogenic Clarireedia spp. Associated with Dollar Spot in Turfgrass

Agronomy ◽

10.3390/agronomy11081489 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1489

Author(s):

Tammy Stackhouse ◽

Sumyya Waliullah ◽

Alfredo D. Martinez-Espinoza ◽

Bochra Bahri ◽

Emran Ali

Keyword(s):

Pcr Primers ◽

The United States ◽

Fungal Species ◽

Dollar Spot ◽

Direct Pcr ◽

Specific Pcr ◽

Specificity And Sensitivity ◽

Pure Cultures ◽

Speed Up ◽

Cleaved Amplified Polymorphic Sequences

Dollar spot is one of the most destructive diseases in turfgrass. The causal agents belong to the genus Clarireedia, which are known for causing necrotic, sunken spots in turfgrass that coalesce into large damaged areas. In low tolerance settings like turfgrass, it is of vital importance to rapidly detect and identify the pathogens. There are a few methods available to identify the genus Clarireedia, but none of those are rapid enough and characterize down to the species level. This study produced a co-dominant cleaved amplified polymorphic sequences (CAPS) test that differentiates between C. jacksonii and C. monteithiana, the two species that cause dollar spot disease within the United States. The calmodulin gene (CaM) was targeted to generate Clarireedia spp. specific PCR primers. The CAPS assay was optimized and tested for specificity and sensitivity using DNA extracted from pure cultures of two Clarireedia spp. and other closely related fungal species. The results showed that the newly developed primer set could amplify both species and was highly sensitive as it detected DNA concentrations as low as 0.005 ng/µL. The assay was further validated using direct PCR to speed up the diagnosis process. This drastically reduces the time needed to identify the dollar spot pathogens. The resulting assay could be used throughout turfgrass settings for a rapid and precise identification method in the US.

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Identification for adulteration of beef with chicken based on single primer-triggered isothermal amplification

International Journal of Food Engineering ◽

10.1515/ijfe-2019-0239 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Jiao Chen ◽

Pansong Zhang ◽

Haixia Wang ◽

Yanjing Shi

Keyword(s):

Limit Of Detection ◽

Chicken Meat ◽

Isothermal Amplification ◽

Work Flow ◽

Acid Extraction ◽

Specificity And Sensitivity ◽

Total Dna ◽

Meat Species ◽

Species Specific ◽

Single Primer

Abstract Adulteration of beef with cheap chicken has become a growing problem worldwide. In this study, a quick, single primer-triggered isothermal amplification (SAMP) combined with a fast nucleic acid extraction method was employed to detect the chicken meat in adulterated beef. Chicken from adulterated beef was identified using the chicken species-specific primer designed according to the Gallus gallus mitochondrial conserved sequences. Our SAMP method displayed good specificity and sensitivity in detecting chicken and beef meat DNA–the limit of detection (LOD) of SAMP is 0.33 pg/μL of chicken and beef total DNA and 2% w/w chicken meat in beef. The whole work flow from DNA extraction to signal detection can be finished within 1 h, fulfilling the requirement of on-site meat species identification.

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