Barcoding the food chain: from Sanger to high-throughput sequencing

Littlefair, Joanne E.; Clare, Elizabeth L.

doi:10.1139/gen-2016-0028

Cited by 28 publications

(22 citation statements)

References 127 publications

(147 reference statements)

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“…DNA barcoding has aided our understanding of species community compositions, food webs and genetic variation within species (Baker et al 2016;Littlefair & Clare 2016;Roslin & Majaneva 2016) and is an important and useful asset in biosecurity (Ashfaq & Hebert 2016;DOI 10.1163/1876312X-00002172 Hodgetts et al 2016) and biomonitoring of freshwater ecosystems (Brodin et al 2013;Carew et al 2013). DNA barcodes can uncover cryptic species diversity (Macher et al 2016;Witt et al 2006;Yang et al 2012), and indicate species boundaries with additional morphological and ecological data.…”

Section: Introductionmentioning

confidence: 99%

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Stur

Ekrem

2018

Insect Syst. Evol.

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For over a decade, DNA barcoding has proven an effective modern tool in taxonomy, evolutionary biology and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. Using DNA barcodes, we uncovered a number of potential species within the Tanytarsus curticornis and Tanytarsus heusdensis species complexes (Diptera: Chironomidae) and detected morphological differences a posteriori that support the description of new species. Unusually large intraspecific divergence in COI p-distance (up to 10%) was observed for two species complexes. In total, eight species new to science are described and figured: T. adustus sp. n., T. heberti sp. n., T. madeiraensis sp. n., T. pseudoheusdensis sp. n., T. songi sp. n., T. thomasi sp. n., T. tongmuensis sp. n. and T. wangi sp. n.. Tanytarsus reei and T. tamaoctavus are redescribed, and T. tusimatneous is listed as a new junior synonym of T. tamaduodecimus. The diagnostic characters of the remaining species of the complexes are discussed. Keys to males and pupae are given.

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Section: Introductionmentioning

confidence: 99%

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Stur

Ekrem

2018

Insect Syst. Evol.

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“…However, DNA‐based techniques will be informative in providing medium‐ to long‐term estimates of dietary contents if DNA persists inside the digestive parts. The use of environmental RNA is also likely to be of interest in the study of pitcher plants due to its shorter half‐life (Littlefair & Clare, ; Pochon, Zaiko, Fletcher, Laroche, & Wood, ), which could possibly discriminate between dead prey and living inquilines in a study such as this. Pitcher plants represent an ideal system to test this in, because their passive feeding strategies can be more easily manipulated than that of active predatory animals.…”

Section: Discussionmentioning

confidence: 99%

DNA metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient

et al. 2018

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Resource variation along abiotic gradients influences subsequent trophic interactions and these effects can be transmitted through entire food webs. Interactions along abiotic gradients can provide clues as to how organisms will face changing environmental conditions, such as future range shifts. However, it is challenging to find replicated systems to study these effects. Phytotelmata, such as those found in carnivorous plants, are isolated aquatic communities and thus form a good model for the study of replicated food webs. Due to the degraded nature of the prey, molecular techniques provide a useful tool to study these communities. We studied the pitcher plant Sarracenia purpurea L. in allochthonous populations along an elevational gradient in the Alps and Jura. We predicted that invertebrate richness in the contents of the pitcher plants would decrease with increasing elevation, reflecting harsher environmental conditions. Using metabarcoding of the COI gene, we sequenced the invertebrate contents of these pitcher plants. We assigned Molecular Operational Taxonomic Units at ordinal level as well as recovering species-level data. We found small but significant changes in community composition with elevation. These recovered sequences could belong to invertebrate prey, rotifer inquilines, pollinators and other animals possibly living inside the pitchers. However, we found no directional trend or site-based differences in MOTU richness with elevational gradient. Use of molecular techniques for dietary or contents analysis is a powerful way to examine numerous degraded samples, although factors such as DNA persistence and the relationship with species presence still have to be completely determined.

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“…Metabarcoding approaches are very powerful to identify an assemblage of parasitoid species within their hosts without any a priori knowledge of potential interaction links between species. However, metabarcoding approaches still require important bioinformatics development to properly quantify trophic interactions, and are not as cheap, fast, and easy to use as the traditional barcoding method [ 56 , 57 ]. The simple molecular methods developed here were based on an a priori knowledge of the parasitoid community.…”

Section: Discussionmentioning

confidence: 99%

Molecular Tools for the Detection and the Identification of Hymenoptera Parasitoids in Tortricid Fruit Pests

Franck

Maalouly-Matar

Olivares

2017

IJMS

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Biological control requires specific tools for the accurate detection and identification of natural enemies in order to estimate variations in their abundance and their impact according to changes in environmental conditions or agricultural practices. Here, we developed two molecular methods of detection based on PCR-RFLP with universal primers and on PCR with specific primers to identify commonly occurring larval parasitoids of the tortricid fruit pests and to estimate parasitism in the codling moth. Both methods were designed based on DNA sequences of the COI mitochondrial gene for a range of parasitoids that emerged from Cydia pomonella and Grapholita molesta caterpillars (102 parasitoids; nine species) and a range of potential tortricid hosts (40 moths; five species) damaging fruits. The PCR-RFLP method (digestion by AluI of a 482 bp COI fragment) was very powerful to identify parasitoid adults and their hosts, but failed to detect parasitoid larvae within eggs or within young C. pomonella caterpillars. The PCR method based on specific primers amplified COI fragments of different lengths (131 to 463 bp) for Ascogaster quadridentata (Braconidae); Pristomerus vulnerator (Ichneumonidae); Trichomma enecator (Ichneumonidae); and Perilampus tristis (Perilampidae), and demonstrated a higher level of sensibility than the PCR-RFLP method. Molecular estimations of parasitism levels in a natural C. pomonella population with the specific primers did not differ from traditional estimations based on caterpillar rearing (about 60% parasitism in a non-treated apple orchard). These PCR-based techniques provide information about within-host parasitoid assemblage in the codling moth and preliminary results on the larval parasitism of major tortricid fruit pests.

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Barcoding the food chain: from Sanger to high-throughput sequencing

Cited by 28 publications

References 127 publications

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

DNA metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient

Molecular Tools for the Detection and the Identification of Hymenoptera Parasitoids in Tortricid Fruit Pests

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