First report of mitochondrial COI in foraminifera and implications for DNA barcoding

Abstract Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S...

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Autores principales:	Jan-Niklas Macher, Jeremy G. Wideman, Elsa B. Girard, Anouk Langerak, Elza Duijm, Jamaluddin Jompa, Aleksey Sadekov, Rutger Vos, Richard Wissels, Willem Renema
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/17f4476ea3e04d9a9a21f68eaa56562c
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spelling	oai:doaj.org-article:17f4476ea3e04d9a9a21f68eaa56562c2021-11-14T12:22:24ZFirst report of mitochondrial COI in foraminifera and implications for DNA barcoding10.1038/s41598-021-01589-52045-2322https://doaj.org/article/17f4476ea3e04d9a9a21f68eaa56562c2021-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-01589-5https://doaj.org/toc/2045-2322Abstract Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.Jan-Niklas MacherJeremy G. WidemanElsa B. GirardAnouk LangerakElza DuijmJamaluddin JompaAleksey SadekovRutger VosRichard WisselsWillem RenemaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jan-Niklas Macher Jeremy G. Wideman Elsa B. Girard Anouk Langerak Elza Duijm Jamaluddin Jompa Aleksey Sadekov Rutger Vos Richard Wissels Willem Renema First report of mitochondrial COI in foraminifera and implications for DNA barcoding
description	Abstract Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.
format	article
author	Jan-Niklas Macher Jeremy G. Wideman Elsa B. Girard Anouk Langerak Elza Duijm Jamaluddin Jompa Aleksey Sadekov Rutger Vos Richard Wissels Willem Renema
author_facet	Jan-Niklas Macher Jeremy G. Wideman Elsa B. Girard Anouk Langerak Elza Duijm Jamaluddin Jompa Aleksey Sadekov Rutger Vos Richard Wissels Willem Renema
author_sort	Jan-Niklas Macher
title	First report of mitochondrial COI in foraminifera and implications for DNA barcoding
title_short	First report of mitochondrial COI in foraminifera and implications for DNA barcoding
title_full	First report of mitochondrial COI in foraminifera and implications for DNA barcoding
title_fullStr	First report of mitochondrial COI in foraminifera and implications for DNA barcoding
title_full_unstemmed	First report of mitochondrial COI in foraminifera and implications for DNA barcoding
title_sort	first report of mitochondrial coi in foraminifera and implications for dna barcoding
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/17f4476ea3e04d9a9a21f68eaa56562c
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First report of mitochondrial COI in foraminifera and implications for DNA barcoding

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