Application of Partial Internal Transcribed Spacer Sequences for the Discrimination of<i>Artemisia capillaris</i>from Other<i>Artemisia</i>Species

Doh, Eui Jeong; Paek, Seung-Ho; Lee, Guemsan; Lee, Mi-Young; Oh, Seung-Eun

doi:10.1155/2016/7043436

Cited by 10 publications

(9 citation statements)

References 30 publications

(54 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Molecular marker techniques based on robust genomic tools could resolve issues in the species delimitation and phylogenetic relationships of Artemisia. As a universal barcode for plants, ITS1, ITS2, and ETS were developed into a sequence-characterized amplified region [50,51] or high-resolution melt markers [52] and applied to Artemisia. However, insufficient sequence polymorphism of the markers and the frequent polyploidy of Artemisia hindered their use for species identification.…”

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

et al. 2020

View full text Add to dashboard Cite

Background: Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge. Results: To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power. Conclusions: The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as superbarcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

show abstract

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Therefore, we tried to develop the DNA marker for Amomi Fructus. The SNP-based DNA Marker has been a successful method to identify the medicinal herbs from its adulterants [36,37,38,39,40]. In the case of Amomi Fructus, the recoded origin species in pharmacopoeia was different according to the country of origin.…”

Section: Discussionmentioning

confidence: 99%

Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

2019

Self Cite

View full text Add to dashboard Cite

Amomi Fructus is one of the traditional medicines derived from the ripe fruits of the Zingiberaceae family of plants, which include Amomum villosum, A. villosum var. xanthioides, and A. longiligulare. Owing to their highly similar morphological traits, several kinds of adulterants of Amomi Fructus have been reported. Therefore, accurate and reliable methods of identification are necessary in order to ensure drug safety and quality. We performed DNA barcoding using five regions (ITS, matK, rbcL, rpoB, and trnL-F intergenic spacer) of 23 Amomi Fructus samples and 22 adulterants. We designed specific DNA markers for Amomi Fructus based on the single nucleotide polymorphisms (SNPs) in the ITS. Amomi Fructus was well separated from the adulterants and was classified with the species of origin based on the detected SNPs from the DNA barcoding results. The AVF1/ISR DNA marker for A. villosum produced a 270 bases amplified product, while the ALF1/ISF DNA marker produced a 350 bases product specific for A. longiligulare. Using these DNA markers, the monitoring of commercially distributed Amomi Fructus was performed, and the monitoring results were confirmed by ITS analysis. This method identified samples that were from incorrect origins, and a new species of adulterant was also identified. These results confirmed the accuracy and efficiency of the designed DNA markers; this method may be used as an efficient tool for the identification and verification of Amomi Fructus.

show abstract

“…COXI exhibit fast mutation rate and easily distinguished between closely related species (Hong et al, 2019), preferred for the evolutionary time depths. Internal Transcribed Spacer primers reveal highest degree of variation along its genomic sequences via unequal crossing over and gene conversion (Eui et al, 2016).…”

Section: Research Articlementioning

confidence: 99%

Molecular Characterization and Phylogenetic Analysis of Babesia Species Isolated from Domestic Cattle

Farooq¹

2020

PVJ

View full text Add to dashboard Cite

Babesiosis is a key tick born disease caused by the protozoal parasites belonging to the genus Babesia, cosmopolitan in nature and infecting enormous range of large ruminants. Study was intended to determine the presence of local isolates of Babesia species (B. bovis, B. bigemina) their molecular characterization and phylogenetic relationship in cattle (district Narowal) Punjab. Blood samples were collected from 200 suspected cattle, from seven villages of selected district. DNA was extracted by using DNA zole, Gene-all Kit, manual method and subjected to PCR for amplification using specific RLB and Universal Primers. Quantification of protozoan parasite was performed by RT PCR using Solis biodine kit. A total of 36 out of 200 animal samples, were found positive by microscopy. PCR positive samples (17) were amplified and bands of strength 520-bp and 800-bp with specific RLB and for universal primers respectively were obtained for Babesia species. These 17 samples were sent for sequencing and by using Clustal W; Bioedit software with Neighbor-joining method phylogenetic tree was established. Current study reported the presence of B. bigemina i.e. 18% (conventional method) in large ruminants of district Narowal, Pakistan, and confirmation by (molecular characterization) PCR (8.5%) and phylogenetic relationship. Phylogenetic results showed that our study has homology with Babesia bigemina strain.

show abstract

Application of Partial Internal Transcribed Spacer Sequences for the Discrimination ofArtemisia capillarisfrom OtherArtemisiaSpecies

Cited by 10 publications

References 30 publications

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

Molecular Characterization and Phylogenetic Analysis of Babesia Species Isolated from Domestic Cattle

Contact Info

Product

Resources

About