DNA Barcoding: Bioinformatics Workflows for Beginners

Wilson, John James; Sing, Kong-Wah; Jaturas, Narong

doi:10.1016/b978-0-12-809633-8.20468-8

Cited by 13 publications

(15 citation statements)

References 22 publications

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“…Although some methods, such as gas chromatography–mass spectrometry fingerprint (Chen et al 2016), fourier transform infrared spectroscopy (Chen et al 2015), capillary electrophoresis (Zha et al 2009) have been applied for the authentication of Dendrobium species, they are complicated needing professional operators, cost- and time-consuming, and hard to distinguish the commercial samples that share similar textures, chemical and microscopic characteristics after processing and preparation as decoction pieces. In recent decades, molecular techniques, such as DNA barcoding (Wilson et al 2019) and real-time PCR (Sobrino-Gregorio et al 2019) have been used to differentiate many closely related species with significant advantages in the fields of taxonomy, phylogeny, evolution and breeding (Teixeira da Silva et al 2016), especially for the morphological analogues or complexes including Dendrobium species. Currently, nuclear sequences [including internal transcribed spacer (ITS), intergenic spacer (IGS)] and plastid genes ( matK , rbcL , psbA - trnH , trnL intron , etc.)…”

Section: Introductionmentioning

confidence: 99%

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis

Fang

Tingmo

et al. 2019

AMB Expr

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Owing to their significant medicinal and edible values, the natural Dendrobium species have underdone over-collection and habitat destruction, and cultivated species emerged for candidates. However, these Dendrobium plants are similar in shape to be easily confused, leading to extreme difficulties for identification based on their morphological and chemical features. In this study, the rDNA ITS region sequence analysis was developed for rapid and accurate identification of thirteen wild and cultivated Dendrobium species belonging to two sections Formosae and Chrysotoxae . By cloning and sequencing the rDNA ITS region genes from 13 Dendrobium species, the phylogenetic relationships among them were analyzed. Results showed that the variation of the ITS region, together with the lengths and Guanine and Cytosine contents of ITS, 5.8s rDNA, ITS1 and ITS2 sequences occurred in the tested Dendrobium species, and which from section Chrysotoxae was higher than that from section Formsae . Phylogenetic analysis based on neighbor-joining and maximum p-arsimony trees indicated that the Dendrobium species of sections Formosae and Chrysotoxae could be well divided into two groups. A majority of Dendrobium species exhibited distinctive ITS2 secondary structures, while for those with close genetic relationships were similar. Therefore, the ITS2 region sequence analysis is simple, quick, and highly reliable that can be used as an effective tool for molecular identification and classification, as well as the reconstruction of the phylogeny of wild and cultivated Dendrobium species belonging to different sections.

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Section: Introductionmentioning

confidence: 99%

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis

Fang

Tingmo

et al. 2019

AMB Expr

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“…DNA barcode fragments of COI mtDNA were amplified (following standard protocols in Wilson 2012 ) using LCO1490/HCO2198 primers. PCR products were Sanger-sequenced and checked for quality (following standard protocols in Wilson et al 2019 ). Specimen data and any generated DNA barcodes were submitted to Barcode of Life Datasystems (BOLD; Ratnasingham and Hebert 2007 ).…”

Section: Sampling Methodsmentioning

confidence: 99%

“…We will (1) generate data from urban parks in megacities across East-Southeast Asia to enable region-wide meta-analyses of butterfly diversity in this rapidly urbanising region (Sing et al 2017); (2) examine the value of urban parks as refuges for butterflies through investigating the relationships between butterfly species richness and the age, size and distance from the central business district of parks in East-Southeast Asian cities (Sing et al 2016a, Sing et al 2016b, Sing et al 2019; (3) identify which type of microhabitat within urban parks provides suitable breeding and foraging habitat for butterflies (Sing et al 2016a, Sing et al 2016b; and (4) contribute to DNA barcode reference libraries of urban butterflies to enable rapid surveys of these species in future studies (Wilson et al 2013).…”

Section: Design Descriptionmentioning

confidence: 99%

Butterflies in urban parks in the Bangkok Metropolitan Region, Thailand

Jaturas¹,

Sing²,

Wilson³

et al. 2020

BDJ

Self Cite

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For residents of East-Southeast Asia’s megacities, interactions with “nature” may be largely limited to interactions taking place in urban parks. Urban parks provide refuges for ecologically-important biodiversity, such as insect pollinators. While residents may be unlikely to notice small insects, butterflies are more likely to be noticed and to provide positive human-“nature” interactions. Engaging residents and city planners in promoting habitat for butterflies is valid conservation practice and has well-understood educational and well-being benefits. Surveying and monitoring is an essential activity to corroborate, improve and communicate the outcomes of conservation practices amongst city governments, scientists and other stakeholders. Here we present the data from a survey of butterflies in urban parks in the megacity of the Bangkok Metropolitan Region as part of the "Urban biodiversity and human well-being in East-Southeast Asia's megacities" project organised by the "Urban Butterflies in Asia Research Network". We recorded 51 species of butterflies from ten urban parks in the Bangkok Metropolitan Region. This was more than double the 25 species reported in Bangkok's City Biodiversity Index application. However, this was lower than that recorded in other megacities in Southeast Asia, such as Kuala Lumpur at 60 species. Most of the butterflies recorded were common and widespread species. DNA barcodes are provided for most of the butterflies sampled.

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“…To tackle this question, DNA barcoding emerged as a universal tool for food traceability based on the identification of a standard region in a given genome (called DNA barcode) that is uniquely associated with a specie, breed/variety or individual. The reasons behind the success of the application of DNA barcoding are related with i) DNA variability study attributed to a taxa, ii) standardization of the protocol (from sample collection to the analysis), and iii) bioinformatic approaches to analyse and effectively divulge the information obtained in public databases (Wilson, Sing, & Jaturas, 2019).…”

Section: Dna Markers and Bioinformatics As Tools To Assist Dairy Products Traceability And Authenticationmentioning

confidence: 99%

DNA-based approaches for dairy products authentication: A review and perspectives

Baptista

Cunha

Domingues

2021

Trends in Food Science & Technology

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Background: Food fraud has become an increasingly worldwide problem mainly driven by rapid innovation in the food sector and constantly changing consumer's choices. This led to an increased necessity to improve/establish reliable authentication processes, resulting in the replacement of protein-based techniques for dairy products authentication by higher sensitive and reproducible DNA-based methods. Most used molecular methods for dairy products authentication include PCR, Real-time PCR, multiplex PCR, and PCR-RFLP. Despite the several molecular methods available for species/breeds differentiation in dairy products, there is a need for the development of more efficient and reliable molecular tools. Scope and approach: In this review, traditional and more recent DNA-based methods for dairy products authentication are discussed and analysed. Moreover, the increasingly important role of bioinformatic tools for analysis of large amount of data and for the development of DNA markers is also discussed. Key findings and conclusions: DNA quality is one of the major factors affecting molecular-based dairy products authentication, which can be influenced by the manufacturing process, extraction method employed, chemical composition of the food matrix, among others. PCR-based methods continue to be the most important and successfully used for dairy products authentication. The DNA markers chosen for species/breed detection are an important factor for PCR success. Although there are several molecular methods for the detection of adulterant species, there is still an unmet demand for methods to detect adulterant breeds. Available public databases and bioinformatics revolutionized the analysis of large amount of data and will be pivotal for the development of effective DNA markers.

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DNA Barcoding: Bioinformatics Workflows for Beginners

Cited by 13 publications

References 22 publications

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis

Butterflies in urban parks in the Bangkok Metropolitan Region, Thailand

DNA-based approaches for dairy products authentication: A review and perspectives

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