The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data

The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such stud...

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Autores principales:	Haris Zafeiropoulos, Laura Gargan, Sanni Hintikka, Christina Pavloudi, Jens Carlsson
Formato:	article
Lenguaje:	EN
Publicado:	Pensoft Publishers 2021
Materias:	Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/9c35018de6ff4c008eb7429e98131129
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spelling	oai:doaj.org-article:9c35018de6ff4c008eb7429e981311292021-11-05T04:30:28ZThe Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data10.3897/mbmg.5.696572534-9708https://doaj.org/article/9c35018de6ff4c008eb7429e981311292021-11-01T00:00:00Zhttps://mbmg.pensoft.net/article/69657/download/pdf/https://mbmg.pensoft.net/article/69657/download/xml/https://mbmg.pensoft.net/article/69657/https://doaj.org/toc/2534-9708The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such studies do not get a taxonomic assignment with a reference sequence. To assess and investigate such sequences, we have developed the Dark mAtteR iNvestigator (DARN) software tool. For this purpose, a reference COI-oriented phylogenetic tree was built from 1,593 consensus sequences covering all the three domains of life. With respect to eukaryotes, consensus sequences at the family level were constructed from 183,330 sequences retrieved from the Midori reference 2 database, which represented 70% of the initial number of reference sequences. Similarly, sequences from 431 bacterial and 15 archaeal taxa at the family level (29% and 1% of the initial number of reference sequences respectively) were retrieved from the BOLD and the PFam databases. DARN makes use of this phylogenetic tree to investigate COI pre-processed sequences of amplicon samples to provide both a tabular and a graphical overview of their phylogenetic assignments. To evaluate DARN, both environmental and bulk metabarcoding samples from different aquatic environments using various primer sets were analysed. We demonstrate that a large proportion of non-target prokaryotic organisms, such as bacteria and archaea, are also amplified in eDNA samples and we suggest prokaryotic COI sequences to be included in the reference databases used for the taxonomy assignment to allow for further analyses of dark matter. DARN source code is available on GitHub at https://github.com/hariszaf/darn and as a Docker image at https://hub.docker.com/r/hariszaf/darn.Haris ZafeiropoulosLaura GarganSanni HintikkaChristina PavloudiJens CarlssonPensoft PublishersarticleEcologyQH540-549.5ENMetabarcoding and Metagenomics, Vol 5, Iss , Pp 163-174 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Ecology QH540-549.5
spellingShingle	Ecology QH540-549.5 Haris Zafeiropoulos Laura Gargan Sanni Hintikka Christina Pavloudi Jens Carlsson The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
description	The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such studies do not get a taxonomic assignment with a reference sequence. To assess and investigate such sequences, we have developed the Dark mAtteR iNvestigator (DARN) software tool. For this purpose, a reference COI-oriented phylogenetic tree was built from 1,593 consensus sequences covering all the three domains of life. With respect to eukaryotes, consensus sequences at the family level were constructed from 183,330 sequences retrieved from the Midori reference 2 database, which represented 70% of the initial number of reference sequences. Similarly, sequences from 431 bacterial and 15 archaeal taxa at the family level (29% and 1% of the initial number of reference sequences respectively) were retrieved from the BOLD and the PFam databases. DARN makes use of this phylogenetic tree to investigate COI pre-processed sequences of amplicon samples to provide both a tabular and a graphical overview of their phylogenetic assignments. To evaluate DARN, both environmental and bulk metabarcoding samples from different aquatic environments using various primer sets were analysed. We demonstrate that a large proportion of non-target prokaryotic organisms, such as bacteria and archaea, are also amplified in eDNA samples and we suggest prokaryotic COI sequences to be included in the reference databases used for the taxonomy assignment to allow for further analyses of dark matter. DARN source code is available on GitHub at https://github.com/hariszaf/darn and as a Docker image at https://hub.docker.com/r/hariszaf/darn.
format	article
author	Haris Zafeiropoulos Laura Gargan Sanni Hintikka Christina Pavloudi Jens Carlsson
author_facet	Haris Zafeiropoulos Laura Gargan Sanni Hintikka Christina Pavloudi Jens Carlsson
author_sort	Haris Zafeiropoulos
title	The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
title_short	The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
title_full	The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
title_fullStr	The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
title_full_unstemmed	The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
title_sort	dark matter investigator (darn) tool: getting to know the known unknowns in coi amplicon data
publisher	Pensoft Publishers
publishDate	2021
url	https://doaj.org/article/9c35018de6ff4c008eb7429e98131129
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The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data

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