Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes

Houdt, J. K. J. Van; Breteler, F.J.; Virgilio, M.; Meyer, M. De

doi:10.1111/j.1755-0998.2009.02800.x

Cited by 74 publications

(92 citation statements)

References 24 publications

(27 reference statements)

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“…Additionally, primers are often developed on a small set of taxa, and thus might not work well for the ecosystem, geographic region or taxa under study. For example, Clarke and co-authors evaluated the L499 + H2123d as a metabarcoding primer (Clarke et al, 2014), but it was originally only developed to target tephritid fruit flies and probably was never intended to be used beyond this dipteran family (Van Houdt et al, 2010). Therefore, careful in silico evaluation and mock community testing of newly developed primers or primers from the literature against the specific taxa of interest is crucial for metabarcoding projects.…”

Section: Primer Success Is Determined By Base Degeneracy and Referencmentioning

confidence: 99%

“…However, the COI barcoding gene region shows high codon degeneracy throughout its sequence, making the design of such "truly" universal primers difficult (Deagle et al, 2014;Sharma and Kobayashi, 2014). Several COI barcoding primers with different levels of base degeneracy have been developed of which many are now used or could be suitable for metabarcoding studies (Figure 1, e.g., Folmer et al, 1994;Hebert et al, 2004;Meusnier et al, 2008;Van Houdt et al, 2010;Shokralla et al, 2011Shokralla et al, , 2015Zeale et al, 2011;Geller et al, 2013;Leray et al, 2013;Gibson et al, 2014;Brandon-Mong et al, 2015). However, often these primers were developed for a specific taxonomic group, purpose or ecosystem, for example the primers by Zeale et al (2011) which were originally developed for gut content analysis on bats but are now more widely used.…”

Section: Introductionmentioning

confidence: 99%

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Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Elbrecht

Leese

2017

Front. Environ. Sci.

223

232

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A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for such bioassessments as many taxa show specific responses to environmental conditions. However, generating accurate macroinvertebrate inventories based on primarily larval morphology is difficult and error-prone. Here, DNA metabarcoding provides new opportunities. Its potential to accurately identify invertebrates in bulk samples to the species level has been demonstrated in several case studies. However, DNA based identification is often limited by primer bias, potentially leading to taxa in the sample remaining undetected. Thus, the success of DNA metabarcoding as an emerging technique for bioassessment critically relies on carefully evaluated primers. We used the R package PrimerMiner to obtain and process cytochrome c oxidase I (COI) sequence data for the 15 globally most relevant freshwater invertebrate groups for stream assessment. Using these sequence alignments, we developed four primer combinations optimized for freshwater macroinvertebrates. All primers were evaluated by sequencing 10 mock community samples, each consisting of 52 freshwater invertebrate taxa. Additionally, popular metabarcoding primers from the literature and the developed primers were tested in silico against these 15 relevant invertebrate groups. The developed primers varied in amplification efficiency and the number of detected taxa, yet, all detected more taxa than standard "Folmer" barcoding primers. Two new primer combinations showed even more consistent amplification than a previously tested ribosomal marker (16S) and detected all 42 insect taxa present in the mock community samples. In silico evaluation revealed critical design flaws in some commonly used primers from the literature. We demonstrate a reliable strategy to develop optimized primers using the tool PrimerMiner. The developed primers detected almost all taxa present in the mock samples, and we argue that high base degeneracy is necessary to decrease primer bias as confirmed by experimental results and in silico primer evaluation. We further demonstrate that some primers currently Elbrecht and Leese Freshwater Primer Development and Evaluation used in metabarcoding studies may not be suitable for amplification of freshwater macroinvertebrates. Therefore, careful primer evaluation and more region/ecosystem specific primers are needed before DNA metabarcoding can be used for routine bioassessment of freshwater ecosystems.

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Section: Primer Success Is Determined By Base Degeneracy and Referencmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Elbrecht

Leese

2017

Front. Environ. Sci.

223

232

View full text Add to dashboard Cite

show abstract

“…These tephritid interceptions were identified to species level using morphological characters and then blind tested by generating a barcode sequence (methods according to [17], [18]) that was compared with the aforementioned regional tephritid library. In this way we verified whether the THR K2P_0.05 threshold calculated from the tephritid reference library could yield a relative ID error <0.05 in a newly generated set of tephritid specimens.…”

Section: Methodsmentioning

confidence: 99%

Identifying Insects with Incomplete DNA Barcode Libraries, African Fruit Flies (Diptera: Tephritidae) as a Test Case

et al. 2012

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We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled relationships between identification performances and distance thresholds in four DNA barcode libraries of Diptera (n = 4270), Lepidoptera (n = 7577), Hymenoptera (n = 2067) and Tephritidae (n = 602 DNA barcodes). In all cases, more restrictive distance thresholds produced a gradual increase in the proportion of true negatives, a gradual decrease of false positives and more abrupt variations in the proportions of true positives and false negatives. More restrictive distance thresholds improved precision, yet negatively affected accuracy due to the higher proportions of queries discarded (viz. having a distance query-best match above the threshold). Using a simple linear regression we calculated an ad hoc distance threshold for the tephritid library producing an estimated relative identification error <0.05. According to the expectations, when we used this threshold for the identification of 188 independently collected tephritids, less than 5% of queries with a distance query-best match below the threshold were misidentified. Ad hoc thresholds can be calculated for each particular reference library of DNA barcodes and should be used as cut-off mark defining whether we can proceed identifying the query with a known estimated error probability (e.g. 5%) or whether we should discard the query and consider alternative/complementary identification methods.

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“…ibol.org/resources/). The utility of DNA barcode data in species discrimination has been demonstrated in different families of Diptera, including Culicidae (Pradeep ), Tephritidae (Van Houdt et al, 2010), Ceratopogonidae (Bakhoum et al, 2013), forensically important species (Nelson et al, 2007). However, similar studies on tabanids are largely wanting.…”

Section: Introductionmentioning

confidence: 99%

Identification through DNA barcoding of Tabanidae (Diptera) vectors of surra disease in India

et al. 2015

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Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes

Cited by 74 publications

References 24 publications

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Identifying Insects with Incomplete DNA Barcode Libraries, African Fruit Flies (Diptera: Tephritidae) as a Test Case

Identification through DNA barcoding of Tabanidae (Diptera) vectors of surra disease in India

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