Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers.
D-loop haplotype
Fish resource estimation
HaCeD-Seq
Nanopore with UMI
Journal
Functional & integrative genomics
ISSN: 1438-7948
Titre abrégé: Funct Integr Genomics
Pays: Germany
ID NLM: 100939343
Informations de publication
Date de publication:
22 Mar 2023
22 Mar 2023
Historique:
received:
01
11
2022
accepted:
06
03
2023
revised:
03
03
2023
entrez:
22
3
2023
pubmed:
23
3
2023
medline:
25
3
2023
Statut:
epublish
Résumé
Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.
Identifiants
pubmed: 36947319
doi: 10.1007/s10142-023-01013-3
pii: 10.1007/s10142-023-01013-3
pmc: PMC10033627
doi:
Substances chimiques
DNA, Environmental
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
96Informations de copyright
© 2023. The Author(s).
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