Idioma:

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

Wood, Susanna A. ; Pochon, Xavier ; Laroche, Olivier ; Ammon, Ulla ; Adamson, Janet ; Zaiko, Anastasija

Molecular ecology resources, 2019-11, Vol.19 (6), p.1407-1419 [Periódico revisado por pares]

England: Wiley Subscription Services, Inc

Texto completo disponível

Citações Citado por

Enviar para

Título:
A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA
Autor: Wood, Susanna A. ; Pochon, Xavier ; Laroche, Olivier ; Ammon, Ulla ; Adamson, Janet ; Zaiko, Anastasija
Assuntos: Animals ; Biofouling ; Chemical analysis ; Communities ; Cytochrome ; Cytochrome-c oxidase ; Cytochromes ; Deoxyribonucleic acid ; DNA ; droplet digital polymerase chain reaction ; Droplets ; Environmental DNA - genetics ; Helminths - genetics ; metabarcoding marine biosecurity ; Occupancy ; Polychaeta - genetics ; Polymerase chain reaction ; quantitative PCR ; Rare species ; Real-Time Polymerase Chain Reaction - methods ; RNA, Ribosomal, 18S - genetics ; rRNA 18S ; Sabella spallanzanii ; Seawater ; Sensitivity and Specificity ; Species Specificity ; Water analysis ; Water sampling
É parte de: Molecular ecology resources, 2019-11, Vol.19 (6), p.1407-1419
Notas: (COI biofouling), and
Data Availability Statement
PRJEB25036
(18S rRNA biofouling). Quantatative PCR and ddPCR copy number and data used for occupancy modelling are available in Table
Raw sequences from the metabarcoding are available in the National Center for Biotechnology Information Sequence Read Archive database under the accession number
PRJNA477646
water
.
PRJNA478269
S2
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Descrição: Targeted species‐specific and community‐wide molecular diagnostics tools are being used with increasing frequency to detect invasive or rare species. Few studies have compared the sensitivity and specificity of these approaches. In the present study environmental DNA from 90 filtered seawater and 120 biofouling samples was analyzed with quantitative PCR (qPCR), droplet digital PCR (ddPCR) and metabarcoding targeting the cytochrome c oxidase I (COI) and 18S rRNA genes for the Mediterranean fanworm Sabella spallanzanii. The qPCR analyses detected S. spallanzanii in 53% of water and 85% of biofouling samples. Using ddPCR S. spallanzanii was detected in 61% of water of water and 95% of biofouling samples. There were strong relationships between COI copy numbers determined via qPCR and ddPCR (water R2 = 0.81, p < .001, biofouling R2 = 0.68, p < .001); however, qPCR copy numbers were on average 125‐fold lower than those measured using ddPCR. Using metabarcoding there was higher detection in water samples when targeting the COI (40%) compared to 18S rRNA (5.4%). The difference was less pronounced in biofouling samples (25% COI, 29% 18S rRNA). Occupancy modelling showed that although the occupancy estimate was higher for biofouling samples (ψ = 1.0), higher probabilities of detection were derived for water samples. Detection probabilities of ddPCR (1.0) and qPCR (0.93) were nearly double metabarcoding (0.57 to 0.27 marker dependent). Studies that aim to detect specific invasive or rare species in environmental samples should consider using targeted approaches until a detailed understanding of how community and matrix complexity, and primer biases affect metabarcoding data.
Editor: England: Wiley Subscription Services, Inc
Idioma: Inglês

Links

View this record in MEDLINE/PubMed

Voltar para lista de resultados

Realização: Logos de Redes Sociais:

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

Wood, Susanna A. ; Pochon, Xavier ; Laroche, Olivier ; Ammon, Ulla ; Adamson, Janet ; Zaiko, Anastasija

England: Wiley Subscription Services, Inc

Buscando em bases de dados remotas. Favor aguardar.