DNA barcoding aids in identification of adulterants of Trillium govanianum Wall. ex D. Don

Islam, Shahid Ul; Dar, Tanvir Ul Hassan; Khuroo, Anzar A.; Bhat, Basharat Ahmad; Mangral, Zahid Ahmed; Tariq, Lubna; Tantray, Wajahat W.; Malik, Akhtar H.

doi:10.1016/j.jarmap.2021.100305

Cited by 12 publications

(9 citation statements)

References 46 publications

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“…Species identification based on morphology is affected by season, environment, and human factors, which may cause results to be unreliable ( Yang et al, 2020 ). In recent years, DNA barcoding has been widely used to promote accurate species identification owing to its clear advantages ( Tegally et al, 2019 ; Phi et al, 2020 ; Islam et al, 2021 ). The ideal DNA barcode would be a single locus that could be universally amplified and sequenced across a broad range of taxa and provide sufficient variation to reliably distinguish among closely related species ( Song et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

“…Over the years, many molecular analyses have provided insights into the species taxonomy and identification. Currently, DNA barcoding such as rbcL , matK , psbA - trnH and ITS sequences ( Potter et al, 2007 ; Fazekas et al, 2008 ; Chen et al, 2013 ; Xin et al, 2013 ; Tegally et al, 2019 ; Phi et al, 2020 ; Islam et al, 2021 ) has been used for species identification. In Fragaria , the study of DNA barcoding dates back to the phylogenetic analysis conducted by Potter et al (2000) using ITS and trnL - trnF sequences, but the authors were unable to completely distinguish among species in this genus.…”

Section: Introductionmentioning

confidence: 99%

“… Njuguna and Bassil (2011) analyzed psbA - trnH and ITS sequences and reported that the two DNA barcoding sequences are not suitable for species identification in Fragaria . Moreover, more and more studies demonstrated that the four universal barcoding sequences were problematic with low bootstrap support and inability to distinguish between species in land plants ( Xin et al, 2013 ; Tegally et al, 2019 ; Phi et al, 2020 ; Islam et al, 2021 ). Therefore, it is urgent to excavate superior DNA barcoding for special land plants, including Fragaria species, utilizing complete cp genomes, which contain more important variation information for taxonomic and phylogenic purposes ( Huang et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)

Cai

Tao

et al. 2021

Front. Plant Sci.

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Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)

Cai

Tao

et al. 2021

Front. Plant Sci.

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“…Compared to the potential markers from nuclear genome, the chloroplast genome derived markers harbored rich gene copies in plants and su cient inter-speci c divergence coupled with low intra-speci c variations [70]. The identi ed highly variable regions of cp genomes could be developed as e cient DNA barcodes and used extensively in rapid species identi cation and large-scale phylogenetic analysis [71,72]. The previous reports have con rmed that seven DNA barcodes selected based on the basis of the cp genomes of Pterocarpus species displayed better discernibility when comparing with the universal barcodes of rbcL, matK, trnH-psbA and trnL-F [73,74].…”

Section: Development Of Molecular Markers For E Cient Species Classi ...mentioning

confidence: 99%

The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: Molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination

Dong

Zhou

Zhu³

et al. 2022

Preprint

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Background Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. Result This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56-57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into three groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. Conclusion Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family.

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“…Moreover, these two loci for the species level exhibited considerable genetic variability and divergence, ease of amplification, short sequence length, conserved flanking sites for developing universal primers, and ease of alignment and species relationship analysis [ 17 ]. Literature reported that psbA-trnH had successfully identified aquatic freshwater plants and the authenticity of herbal medicines accurately and effectively [ 18 , 19 ]. Niu sequenced psbA-trnH and 8 other chloroplast loci of 16 individuals of Triplostegia that represented the entire distribution range of both species recognized [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding

Yao

Runfang²,

Liu³

et al. 2022

PLoS ONE

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DNA barcoding is a supplementary tool in plant systematics that is extensively used to resolve species-level controversies. This study assesses the significance of using two DNA barcoding loci (e.g., psbA-trnH and trnC-petN) in distinguishing 33 plant samples of the genus Syringa. Results showed that the average genetic distance K2P of psbA-trnH DNA marker was 0.0521, which is much higher than that of trnC-petN, which is 0.0171. A neighbor-joining phylogenetic tree based on psbA-trnH and trnC-petN indicated that the identification rate of psbA-trnH and trnC-petN alone were 75% and 62.5%, respectively. The barcode combination of psbA-trnH+trnC-petN could identify 33 samples of the genus Syringa accurately and effectively with an identification rate of 87.5%. The 33 Syringa samples were divided into four groups: Group I is series Syringa represented by Syringa oblata; Group II is series Villosae represented by Syringa villosa; Group III is series Pubescentes represented by Syringa meyeri; and Group IV is section Ligustrina represented by Syringa reticulata subsp. pekinensis. These research results provided strong evidence that the combinatorial barcode of psbA-trnH+trnC-petN had high-efficiency identification ability and application prospects in species of the genus Syringa.

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DNA barcoding aids in identification of adulterants of Trillium govanianum Wall. ex D. Don

Cited by 12 publications

References 46 publications

Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)

Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)

The complete chloroplast genomes of Tetrastigma hemsleyanum (Vitaceae) from different regions of China: Molecular structure, comparative analysis and development of DNA barcodes for its geographical origin discrimination

Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding

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