Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters

The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. T...

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Autores principales:	Maurizio Pinna, Benedetta Saccomanno, Gabriele Marini, Francesco Zangaro, Akbota Kabayeva, Mina Khalaj, Laura Shaimardan, Simona D’Attis, Eftychia Tzafesta, Valeria Specchia
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	benthic macroinvertebrates DNA-based methods incomplete DNA barcode reference libraries Mediterranean transitional waters ecological status assessment biomonitoring programs Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/9d9ee89aa7cc4555b9251c01a6570b6a
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spelling	oai:doaj.org-article:9d9ee89aa7cc4555b9251c01a6570b6a2021-11-25T16:46:55ZTesting the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters10.3390/biology101110922079-7737https://doaj.org/article/9d9ee89aa7cc4555b9251c01a6570b6a2021-10-01T00:00:00Zhttps://www.mdpi.com/2079-7737/10/11/1092https://doaj.org/toc/2079-7737The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. The morphological identification of benthic macroinvertebrates is the current tool for their assessment. Recently, DNA-based tools have been proposed as effective alternatives. The main current limits of DNA-based applications include the incompleteness of species recorded in the DNA barcode reference libraries and the primers bias. Here, we analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species. The ecological quality status assigned through the potential application of both approaches to the analysed transitional water ecosystems was different in 27% of sites. We also analysed the inter-specific genetic distances to evaluate the potential application of the DNA metabarcoding method. Overall, this work highlights the importance to expand the barcode databases and to analyse, at the regional level, the gaps in the DNA barcodes.Maurizio PinnaBenedetta SaccomannoGabriele MariniFrancesco ZangaroAkbota KabayevaMina KhalajLaura ShaimardanSimona D’AttisEftychia TzafestaValeria SpecchiaMDPI AGarticlebenthic macroinvertebratesDNA-based methodsincomplete DNA barcode reference librariesMediterranean transitional watersecological status assessmentbiomonitoring programsBiology (General)QH301-705.5ENBiology, Vol 10, Iss 1092, p 1092 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	benthic macroinvertebrates DNA-based methods incomplete DNA barcode reference libraries Mediterranean transitional waters ecological status assessment biomonitoring programs Biology (General) QH301-705.5
spellingShingle	benthic macroinvertebrates DNA-based methods incomplete DNA barcode reference libraries Mediterranean transitional waters ecological status assessment biomonitoring programs Biology (General) QH301-705.5 Maurizio Pinna Benedetta Saccomanno Gabriele Marini Francesco Zangaro Akbota Kabayeva Mina Khalaj Laura Shaimardan Simona D’Attis Eftychia Tzafesta Valeria Specchia Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters
description	The ecological assessment of European aquatic ecosystems is regulated under the framework directives on strategy for water and marine environments. Benthic macroinvertebrates are the most used biological quality element for ecological assessment of rivers, coastal-marines, and transitional waters. The morphological identification of benthic macroinvertebrates is the current tool for their assessment. Recently, DNA-based tools have been proposed as effective alternatives. The main current limits of DNA-based applications include the incompleteness of species recorded in the DNA barcode reference libraries and the primers bias. Here, we analysed the influence of the incompleteness of DNA barcode databases on species diversity indices, ecological indicators, and ecological assessment in transitional waters of the southeast Mediterranean, taking into account the availability of commonly sequenced and deposited genomic regions for listed species. The ecological quality status assigned through the potential application of both approaches to the analysed transitional water ecosystems was different in 27% of sites. We also analysed the inter-specific genetic distances to evaluate the potential application of the DNA metabarcoding method. Overall, this work highlights the importance to expand the barcode databases and to analyse, at the regional level, the gaps in the DNA barcodes.
format	article
author	Maurizio Pinna Benedetta Saccomanno Gabriele Marini Francesco Zangaro Akbota Kabayeva Mina Khalaj Laura Shaimardan Simona D’Attis Eftychia Tzafesta Valeria Specchia
author_facet	Maurizio Pinna Benedetta Saccomanno Gabriele Marini Francesco Zangaro Akbota Kabayeva Mina Khalaj Laura Shaimardan Simona D’Attis Eftychia Tzafesta Valeria Specchia
author_sort	Maurizio Pinna
title	Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters
title_short	Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters
title_full	Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters
title_fullStr	Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters
title_full_unstemmed	Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters
title_sort	testing the influence of incomplete dna barcode libraries on ecological status assessment of mediterranean transitional waters
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/9d9ee89aa7cc4555b9251c01a6570b6a
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Testing the Influence of Incomplete DNA Barcode Libraries on Ecological Status Assessment of Mediterranean Transitional Waters

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