ArticleBMC evolutionary biology2013
Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation.
Article in BMC evolutionary biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Phylogenomic analysis and molecular identification of true fruit flies.Frontiers in genetics · 2024Article
- Utilisation of a mitochondrial intergenic region for species differentiation of fruit flies (Diptera: Tephritidae) in South Africa.BMC genomics · 2022Article
- A multiplex PCR assay for the identification of fruit flies (Diptera: Tephritidae) of economic importance in South Africa.Scientific reports · 2022Article
- Vast Gene Flow among the Spanish Populations of the PestInsects · 2022Article
- Partial Ribosomal Nontranscribed Spacer Sequences Distinguish Rhagoletis zephyria (Diptera: Tephritidae) From the Apple Maggot, R. pomonella.Journal of economic entomology · 2022Article
- Article
- Hybridization, Behavioral Patterns, and Pre- and Postzygotic Isolation Between Two Recently Derived Species of Walnut-Infesting Rhagoletis Fruit Flies in the Highlands of Mexico.Neotropical entomology · 2021Article
- Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the GenusFrontiers in plant science · 2020Article
- Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs.PloS one · 2020Article
- Τhe Complete Mitochondrial Genome ofInsects · 2019Article
- Fruit fly identification, population dynamics and fruit damage during fruiting seasons of sweet oranges in Rusitu Valley, Zimbabwe.Scientific reports · 2019Article
- A conserved motif within cox 2 allows broad detection of economically important fruit flies (Diptera: Tephritidae).Scientific reports · 2018Article
- Development of species diagnostic SNP markers for quality control genotyping in four rice (Molecular breeding : new strategies in plant improvement · 2018Article
- Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing.Genome biology and evolution · 2017Article
- The chromosomes and the mitogenome of Ceratitis fasciventris (Diptera: Tephritidae): two genetic approaches towards the Ceratitis FAR species complex resolution.Scientific reports · 2017Article
- The status ofMitochondrial DNA. Part B, Resources · 2016Article
- Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics.Scientific reports · 2016Article
- Article
- Article
- The Bactrocera dorsalis species complex: comparative cytogenetic analysis in support of Sterile Insect Technique applications.BMC genetics · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5'end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination.
resultsIn order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established "near-minimal" sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively.
conclusionsWe found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence represent an important resource for developing taxon-specific diagnostic assays. For selected cases, possible explanations that may cause composite OTUs are discussed.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.