Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment

Chu, Ka Hou; Li, C. P.; Qi, Ji

doi:10.1093/bioinformatics/btl146

Cited by 39 publications

(33 citation statements)

References 52 publications

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“…Previously described nuclear barcode markers (e.g. 28S) may be too long for sequencing with NGS (Chu, Li, & Qi, 2006), while other recently published mini-barcode solutions were adaptations of existing mitochondrial barcode targets, COI (Shokralla et al., 2015) and the 16S ribosomal RNA (Armani et al., 2015a, Armani et al., 2015b, Muñoz-Colmenero et al., 2017). …”

Section: Discussionmentioning

confidence: 99%

Novel nuclear barcode regions for the identification of flatfish species

et al. 2017

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The development of an efficient seafood traceability framework is crucial for the management of sustainable fisheries and the monitoring of potential substitution fraud across the food chain. Recent studies have shown the potential of DNA barcoding methods in this framework, with most of the efforts focusing on using mitochondrial targets such as the cytochrome oxidase 1 and cytochrome b genes. In this article, we show the identification of novel targets in the nuclear genome, and their associated primers, to be used for the efficient identification of flatfishes of the Pleuronectidae family. In addition, different in silico methods are described to generate a dataset of barcode reference sequences from the ever-growing wealth of publicly available sequence information, replacing, where possible, labour-intensive laboratory work. The short amplicon lengths render the analysis of these new barcode target regions ideally suited to next-generation sequencing techniques, allowing characterisation of multiple fish species in mixed and processed samples. Their location in the nucleus also improves currently used methods by allowing the identification of hybrid individuals.

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Section: Discussionmentioning

confidence: 99%

Novel nuclear barcode regions for the identification of flatfish species

et al. 2017

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“…A DNA barcode is a short standardised sequence of DNA that can be used as a genetic maker for species identification [11,13]. Early studies on DNA barcoding have used the nuclear internal transcribed spacer 2 [14], cytochrome b oxidase [15,16], 12S rRNA [17,18] and nicotinamide adenine dinucleotide dehydrogenase [19,20] as target genes. In recent years, however, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene has gained increasing popularity, primarily because of the ease of using a universal set of primers to amplify the gene and its ability to provide a higher sequence variation at inter-species than at intra-species level [10].…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding: complementing morphological identification of mosquito species in Singapore

Chan

Chiang²,

Hapuarachchi

et al. 2014

Parasites & Vectors

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Background: Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the morphological identification of mosquito specimens with their differentiation based on COI barcode, in order to establish a more reliable identification system for mosquito species found in Singapore. Methods: We analysed 128 adult mosquito specimens, belonging to 45 species of 13 genera. Phylogenetic trees were constructed for Aedes, Anopheles, Culex and other genera of mosquitoes and the distinctive clustering of different species was compared with their taxonomic identity. Results: The COI-based DNA barcoding achieved a 100% success rate in identifying the mosquito species. We also report COI barcode sequences of 16 mosquito species which were not available previously in sequence databases. Conclusions: Our study utilised for the first time DNA barcoding to identify mosquito species in Singapore. COI-based DNA barcoding is a useful tool to complement taxonomy-based identification of mosquito species.

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“…Base insertions and deletions (indels) are common in rDNA sequences and do not correlate with phenotype. 31 Therefore, rDNA cannot be used to unambiguously discriminate at the species level specific characteristics such as pathogenesis, drug resistance, and toxin production. In addition, rDNA sequences grouped into operational taxonomic units (OTUs) using an arbitrary limit of sequence conservation are controversial and cannot resolve differences between strains.…”

Section: Challengesmentioning

confidence: 99%

Bioinformatics for Biodefense: Challenges and Opportunities

Valdivia-Granda¹

2010

Biosecurity and Bioterrorism: Biodefense Strategy, Practice, an

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The intentional release of traditional or combinatorial bioweapons remains one of the most important challenges that will continue to shape homeland security. The misuse of dual-use and how-to methods and techniques in the fields of molecular, synthetic, and computational biology can lessen the technical barriers for launching attacks, even for small groups or individuals. Bioinformatics is guiding the implementation of several biodefense countermeasures. However, existing algorithms have not effectively translated available pathogen genomic data into standardized diagnostics, rational vaccine development, or broad spectrum therapeutics. Despite its potential, bioinformatics has a limited impact on forensic and intelligence operations. More than 12 biodefense databases and information exchange architectures lack interoperability and a common layer that restricts scalability and the development of biodefense enterprises. Therefore, in order to use next-generation genome sequencing for medical intelligence, forensic operations, biothreat awareness, and mitigation, the attention has to be redirected toward the development of computational biology applications. This article debates some of the challenges that the bioinformatics field confronts in terms of biodefense problems and proposes potential opportunities to use pathogen genomic data. Issues related to the analysis of pathogen genomes and emerging methods including genomic barcoding, active curation, and knowledge management and their impact on intelligence, forensics, and policymaking are discussed.

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Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment

Abstract: The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server http://cvtree.cbi.pku.edu.cn.

Cited by 39 publications

References 52 publications

Novel nuclear barcode regions for the identification of flatfish species

Novel nuclear barcode regions for the identification of flatfish species

DNA barcoding: complementing morphological identification of mosquito species in Singapore

Bioinformatics for Biodefense: Challenges and Opportunities

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