Sliding Window Analyses for Optimal Selection of Mini-Barcodes, and Application to 454-Pyrosequencing for Specimen Identification from Degraded DNA

Boyer, Stéphane; Brown, Samuel D. J.; Collins, Rupert A.; Cruickshank, Robert; Lefort, Marie‐Caroline; Malumbres‐Olarte, Jagoba; Wratten, Stephen D.

doi:10.1371/journal.pone.0038215

Cited by 46 publications

(43 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Long DNA barcode sequences are no longer considered essential, since even a few base pairs may be sufficiently informative in solving taxonomical questions (see Hajibabaei et al, 2006). The use of such a minibarcode has been proposed as an alternative when it is not possible to obtain the entire fragment because of the degraded nature of the samples (Boyer et al, 2012). Our data further demonstrates that mini-barcodes can be as effective as the entire COI gene in determining species identities.…”

Section: Discussionmentioning

confidence: 66%

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Silva

Malabarba

2017

Neotrop. ichthyol.

View full text Add to dashboard Cite

Accurate identification is essential for any study exploring biodiversity. Unfortunately, museum type specimens preserved for more than a hundred years are often not informative enough for precise identification of the species represented by the name-bearing type. The use of ancient DNA can help solve taxonomic problems when name-bearing types no longer have diagnostic morphological features that allow for an accurate identification of the species involved. That is the case for Deuterodon pedri, an endemic species from a small drainage in the rio Doce basin in Minas Gerais, Brazil, for which the type material is in poor condition. Specimens of D. pedri were collected in 1865 by the Thayer Expedition to Brazil and fixed in spirits, enabling them to yield viable DNA. As the morphology alone of the type material does not allow for an accurate identification, we used both morphological and ancient DNA (aDNA) methods to decisively establish the identity of D. pedri. This identification allowed us to recognize the species among recently collected specimens and then, based on them, redescribe the species. A genetype for the lectotype of D. pedri is presented.Keywords: Lectogenetype, Mini-Barcode, Primers, Rio Doce, Thayer Expedition.Uma identificação acurada é fundamental para qualquer estudo que explora a biodiversidade. Infelizmente, espécimes de museu descritos há mais de cem anos, algumas vezes não são informativos o suficiente para uma identificação precisa da espécie representada pelo tipo. O uso de DNA antigo pode ajudar a resolver problemas taxonômicos, quando espécimes tipos não apresentam mais as características morfológicas diagnósticas que permitem a identificação precisa das espécies. Esse é o caso de Deuterodon pedri, uma espécie endêmica de uma pequena drenagem na bacia do rio Doce, em Minas Gerais, Brasil cujo material tipo encontra-se em condições precárias. Espécimes de D. pedri foram coletados em 1865 pela Expedição Thayer ao Brasil e fixados em "cachaça", o que permite apresentar DNA viável. Como apenas o exame morfológico do material tipo não permitiria a identificação precisa, nós usamos ambos os dados de análises morfológicas e DNA antigo (aDNA) para estabelecer decisivamente a identidade de D. pedri. Esta identificação permitiu reconhecer a espécie entre exemplares coletados recentemente e, com base neles, redescrever a espécie. É apresentado um genetipo para o lectótipo de D. pedri.

show abstract

Section: Discussionmentioning

confidence: 66%

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Silva

Malabarba

2017

Neotrop. ichthyol.

View full text Add to dashboard Cite

show abstract

“…The circularity of mitochondrial genomes is not yet taken into account, which could lead to reconstruction problems. For complex, unknown samples, it would be interesting to use profiles from known mitochondrial genomes to assemble reads on these profiles - the number of different species/contigs could then be estimated from counts of different reads/contigs within a sliding window along the profile(s), or even without any bioinformatics consolidation at all [93]. However such assembly tools have yet to be developed.…”

Section: Resultsmentioning

confidence: 99%

“…For studies based on degraded DNA, availability of reference identification datasets covering the whole mitogenome would provide sequence data to explore alternative markers more suited to each group, and help in the development of primers for divergent groups [93].…”

Section: Resultsmentioning

confidence: 99%

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes

et al. 2012

View full text Add to dashboard Cite

BackgroundResearchers sorely need markers and approaches for biodiversity exploration (both specimen linked and metagenomics) using the full potential of next generation sequencing technologies (NGST). Currently, most studies rely on expensive multiple tagging, PCR primer universality and/or the use of few markers, sometimes with insufficient variability.Methodology/Principal FindingsWe propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.Conclusions/SignificanceThis approach generates large mitogenome datasets. These sequences are useful for phylogenetics, molecular identification and molecular ecology studies, and are compatible with all existing projects or available datasets based on mitochondrial sequences, such as the Barcode of Life project. Our method can yield sequences both from identified samples and metagenomic samples. The use of the same datasets for both kinds of studies makes for a powerful approach, especially since the datasets have a high variability even at species level, and would be a useful complement to the less variable 18S rDNA currently prevailing in metagenomic studies.

show abstract

“…The sliding window function available in the R package SPIDER (Species Identity and Evolution in R) [42] was used to determine the shortest DNA fragment or ‘mini-barcode’ that displayed enough variability to accurately identify all earthworm species occurring in the snails’ geographic range [43]. The selected mini-barcode was a 134 bp fragment starting at position 11922 of the published Lumbricus terrestris Linnaeus mitochondrial genome sequence [44].…”

Section: Methodsmentioning

confidence: 99%

Using Next-Generation Sequencing to Analyse the Diet of a Highly Endangered Land Snail (Powelliphanta augusta) Feeding on Endemic Earthworms

et al. 2013

Self Cite

View full text Add to dashboard Cite

Predation is often difficult to observe or quantify for species that are rare, very small, aquatic or nocturnal. The assessment of such species’ diet can be conducted using molecular methods that target prey DNA remaining in predators’ guts and faeces. These techniques do not require high taxonomic expertise, are applicable to soft-bodied prey and allow for identification at the species level. However, for generalist predators, the presence of mixed prey DNA in guts and faeces can be a major impediment as it requires development of specific primers for each potential prey species for standard (Sanger) sequencing. Therefore, next generation sequencing methods have recently been applied to such situations. In this study, we used 454-pyrosequencing to analyse the diet of Powelliphantaaugusta , a carnivorous landsnail endemic to New Zealand and critically endangered after most of its natural habitat has been lost to opencast mining. This species was suspected to feed mainly on earthworms. Although earthworm tissue was not detectable in snail faeces, earthworm DNA was still present in sufficient quantity to conduct molecular analyses. Based on faecal samples collected from 46 landsnails, our analysis provided a complete map of the earthworm-based diet of P . augusta . Predated species appear to be earthworms that live in the leaf litter or earthworms that come to the soil surface at night to feed on the leaf litter. This indicates that P . augusta may not be selective and probably predates any earthworm encountered in the leaf litter. These findings are crucial for selecting future translocation areas for this highly endangered species. The molecular diet analysis protocol used here is particularly appropriate to study the diet of generalist predators that feed on liquid or soft-bodied prey. Because it is non-harmful and non-disturbing for the studied animals, it is also applicable to any species of conservation interest.

show abstract

Sliding Window Analyses for Optimal Selection of Mini-Barcodes, and Application to 454-Pyrosequencing for Specimen Identification from Degraded DNA

Cited by 46 publications

References 57 publications

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)

Conveniently Pre-Tagged and Pre-Packaged: Extended Molecular Identification and Metagenomics Using Complete Metazoan Mitochondrial Genomes

Using Next-Generation Sequencing to Analyse the Diet of a Highly Endangered Land Snail (Powelliphanta augusta) Feeding on Endemic Earthworms

Contact Info

Product

Resources

About