Internal transcribed spacer 2 (<scp>ITS</scp>2) barcodes: A useful tool for identifying Chinese <i>Zanthoxylum</i>

Zhao, Lili; Feng, Shijing; Tian, Jieyun; Wei, Anzhi; Yang, Tianbo

doi:10.1002/aps3.1157

Cited by 32 publications

(28 citation statements)

References 43 publications

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“…Citrus [24]. However, at the cultivar level, this technique often fails to yield clear results, as exemplified by the study on Zanthoxylum by Zhao et al [25]. Nevertheless, the findings of the present study indicate that at the level of both species and variety, there appears to be relatively low genetic diversity among the three species Z. bungeanum, Z. armatum, and Z. piperitum.…”

Section: Genetic Diversity Assessmentmentioning

confidence: 51%

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Comparative transcriptomes and genetic diversity assessment of two Sichuan peppers (Zanthoxylum bungeanum and Zanthoxylum armatum)

Deng

Liu²,

Gong³

et al. 2019

Preprint

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Background: Species of Zanthoxylum (Sichuan pepper) are diverse and valuable economic trees that have been cultivated across Asia for thousands of years for their aromatic and medicinal properties. The current lack of transcriptome and EST-SSR data for these species represents a constraint with regards to identifying increasingly more diverse cultivars in China. This study was conducted to compare the transcriptome profiles of two Zanthoxylum species (Z. bungeanum and Z. armatum) and develop the EST-SSR markers to assess the genetic diversity in Sichuan pepper. Results: A total of 36.76 G high-quality clean data were screened for subsequent analysis. For Z. bungeanum and Z. armatum, 64,944 and 75,669 unigenes were obtained, respectively. After comparing different databases, we found that the highest number of unigenes (43,3198 and 49,638 for Z. bungeanum and Z. armatum, respectively) were annotated using the NR database. In addition, six pairs of EST-SSR markers were selected to determine the genetic diversity of 125 samples of three Zanthoxylum species. A population clustering dendrogram indicated that there was an average of four samples per population, with the number of allelic genes (Na) ranging from 1 to 1.4510 (average of 1.1462). The number of effective allelic genes (Ne) ranged from 1 to 1.2744 (average of 1.0971), whereas genetic diversity (Nei) ranged from 0 to 0.1486 (average of 0.05512) and Shannon genetic diversity (I) ranged from 0 to 0.2177 (average 0.08123). In individual clustering dendrograms, the 125 samples were divided into five cohorts. Cohort I contained Z. bungeanum and its varieties, cohort II included Z. armatum and its varieties, cohort III contained mostly Z. piperitum and two other Z. bungeanum samples, and cohorts IV and V each contained only two samples, with genetic distances of 0 to 1.14 between them. Conclusion: In this study, we analyzed the comparative transcriptome data of two Zanthoxylum species, for which we assessed genetic diversity using EST-SSR primers derived from their EST information. The genetic diversity of 125 samples obtained from the three Zanthoxylum species Z. bungeanum, Z. armatum and Z. piperitum was relatively low, which can probably be attributed to apomixis.

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Section: Genetic Diversity Assessmentmentioning

confidence: 51%

“…2a. 25,520 isogenes were annotated to one of these five pathways. Of those isogenes annotated, the highest number (12,085) were assigned to cohort A and accounted for 47.36% all isogenes.…”

Section: Kegg Pathwaysmentioning

confidence: 99%

Comparative transcriptomes and genetic diversity assessment of two Sichuan peppers (Zanthoxylum bungeanum and Zanthoxylum armatum)

Deng

Liu²,

Gong³

et al. 2019

Preprint

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“…Zanthoxylum formed a phylogenetic group in previous molecular phylogenetic studies [5,15,16]; however, these studies did not sufficiently resolve the relationships among some of its taxa. These studies were based on the ITS sequences of nuclear ribosomal DNA and the trnL-trnF, matK-trnK, atpB, atp-rbcL, and rbcL sequences of the cp genome [23][24][25]. Although these regions were considered to be universal DNA barcodes for higher plants, they did not allow the assessment of the usefulness of these loci in the barcoding of some taxa.…”

Section: Discussionmentioning

confidence: 99%

Development and Application of InDel Markers for Authentication of the Korean Herbs Zanthoxylum schinifolium and Zanthoxylum piperitum

Kim¹,

Shin²,

Cho

et al. 2019

Foods

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Zanthoxylum schinifolium and Zanthoxylum piperitum are the sources of the well-known traditional Korean herbal medicines “sancho” (prickly ash) and “chopi” (Korean pepper), respectively. Sancho and chopi are often indiscriminately mixed due to the similar appearance of the herbal materials when used as spices and herbal medicines. Moreover, commercial sancho and chopi products often contain adulterants, which is insufficient to ensure food efficacy and safety. In this study, we developed hypervariable insertion/deletion (InDel) markers to distinguish between sancho and chopi products by comparing the complete chloroplast genome sequences of four Zanthoxylum species deposited in the National Center for Biotechnology Information (NCBI) GenBank. Comparative analyses of the nucleotide diversity (Pi) of these Zanthoxylum genomes revealed four hypervariable divergent sites (trnH-psbA, psbZ-trnG, trnfM-rps14, and trnF-ndhK) with Pi > 0.025 among 520 windows. Of these four regions, including two genic and two intergenic regions, only psbZ-trnG yielded accurate PCR amplification results between commercial sancho and chopi products from the Korean herbal medicine market. We therefore selected psbZ-trnG, an InDel-variable locus with high discriminatory powers, as a candidate DNA barcode locus. This InDel marker could be used as a valuable, simple, and efficient tool for identifying these medicinal herbs, thereby increasing the safety of these spices and herbal materials in the food market.

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“…Previous literature showed that the ITS-2 region has been used as a genetic marker for scrutinizing the diversity and exploring phylogenetic relationships 17 among astigmatid mites. ITS-2 marker has been used to successfully verify the taxonomy of closely related species and to differentiate and identify 18,19 different species of astigmatid mites. In this study, we used ITS-2 region to characterize astigmatid mites i.e.…”

Section: Phylogenetic Analysis Of Astigmatid Mites Sarcoptes Scabiei mentioning

confidence: 99%

Phylogenetic Analysis of Astigmatid Mites Sarcoptes scabiei and Dermatophagoides farinae using ITS-2 as a Genetic Marker

Naz

Chaudhry

Rizvi

et al. 2020

L&S

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Objective: The coding of astigmatid mites based on their morphological and developmental characteristics often leads to uncertainty in the results. The ribosomal internal transcribed spacer (ITS-2) region, being highly conserved in eukaryotes is commonly employed as a barcode for identification of mite species. The present study was an attempt to characterize the gene sequences of astigmatid mites i.e. Sarcoptes scabiei (S. scabiei), Dermatophagoides farinae (D. farinae) using ITS-2 as a genetic marker. Place and Duration of Study: The study was conducted at Department of Dermatology, Military Hospital (MH), Rawalpindi from September 2012 to October 2013. Materials and Methods: In order to characterize relationship of astigmatid mites, the ITS-2 marker was successfully amplified and sequenced. The resulting ITS-2 gene sequences were aligned using Clustal W. MEGA 7 was used to construct phylogenetic tree of the aligned sequence. Results: The phylogenetic tree showed an overall genetic distance of 0.53 indicating close genetic relationship among astigmatid mite species. Pairwise distance was calculated for the ITS-2 gene and low genetic diversity values were observed within S. scabiei and D. farinae that range from 0.003-0.008 and 0.006-0.038 respectively. Conclusion: The study supports the view that the ITS-2 region can be used to identify morphologically difficult astigmatid mites but is not useful in characterization of different species based on the geographical distribution. This study has important implication in our understanding of the epidemiology of S. scabiei and D. farinae and development of control strategies in human transmission.

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Internal transcribed spacer 2 (ITS2) barcodes: A useful tool for identifying Chinese Zanthoxylum

Cited by 32 publications

References 43 publications

Comparative transcriptomes and genetic diversity assessment of two Sichuan peppers (Zanthoxylum bungeanum and Zanthoxylum armatum)

Comparative transcriptomes and genetic diversity assessment of two Sichuan peppers (Zanthoxylum bungeanum and Zanthoxylum armatum)

Development and Application of InDel Markers for Authentication of the Korean Herbs Zanthoxylum schinifolium and Zanthoxylum piperitum

Phylogenetic Analysis of Astigmatid Mites Sarcoptes scabiei and Dermatophagoides farinae using ITS-2 as a Genetic Marker

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