Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera
Traditional morphological methods for species identification are highly time consuming, especially for small organisms, such as Foraminifera, a group of shell-building microbial eukaryotes. To analyze large amounts of samples more efficiently, species identification methods have extended to molecula...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2022.809659/full |
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| author | Elsa B. Girard Elsa B. Girard Anouk Langerak Jamaluddin Jompa Owen S. Wangensteen Jan-Niklas Macher Willem Renema Willem Renema |
| author_facet | Elsa B. Girard Elsa B. Girard Anouk Langerak Jamaluddin Jompa Owen S. Wangensteen Jan-Niklas Macher Willem Renema Willem Renema |
| author_sort | Elsa B. Girard |
| collection | DOAJ |
| description | Traditional morphological methods for species identification are highly time consuming, especially for small organisms, such as Foraminifera, a group of shell-building microbial eukaryotes. To analyze large amounts of samples more efficiently, species identification methods have extended to molecular tools in the last few decades. Although a wide range of phyla have good markers available, for Foraminifera only one hypervariable marker from the ribosomal region (18S) is widely used. Recently a new mitochondrial marker cytochrome oxidase subunit 1 (COI) has been sequenced. Here we investigate whether this marker has a higher potential for species identification compared to the ribosomal marker. We explore the genetic variability of both the 18S and COI markers in 22 benthic foraminiferal morphospecies (orders Miliolida and Rotaliida). Using single-cell DNA, the genetic variability within specimens (intra) and between specimens (inter) of each species was assessed using next-generation sequencing. Amplification success rate was twice as high for COI (151/200 specimens) than for 18S (73/200 specimens). The COI marker showed greatly decreased intra- and inter-specimen variability compared to 18S in six out of seven selected species. The 18S phylogenetic reconstruction fails to adequately cluster multiple species together in contrast to COI. Additionally, the COI marker helped recognize misclassified specimens difficult to morphologically identify to the species level. Integrative taxonomy, combining morphological and molecular characteristics, provides a robust picture of the foraminiferal species diversity. Finally, we suggest the use of a set of sequences (two or more) to describe species showing intra-genomic variability additionally to using multiple markers. Our findings highlight the potential of the newly discovered mitochondrial marker for molecular species identification and metabarcoding purposes. |
| first_indexed | 2024-04-11T19:37:20Z |
| format | Article |
| id | doaj.art-7853e098a06646c690b0a76822c9fb60 |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-04-11T19:37:20Z |
| publishDate | 2022-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-7853e098a06646c690b0a76822c9fb602022-12-22T04:06:48ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452022-02-01910.3389/fmars.2022.809659809659Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in ForaminiferaElsa B. Girard0Elsa B. Girard1Anouk Langerak2Jamaluddin Jompa3Owen S. Wangensteen4Jan-Niklas Macher5Willem Renema6Willem Renema7Naturalis Biodiversity Center, Leiden, NetherlandsIBED, University of Amsterdam, Amsterdam, NetherlandsNaturalis Biodiversity Center, Leiden, NetherlandsMarine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar, IndonesiaNorwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, NorwayNaturalis Biodiversity Center, Leiden, NetherlandsNaturalis Biodiversity Center, Leiden, NetherlandsIBED, University of Amsterdam, Amsterdam, NetherlandsTraditional morphological methods for species identification are highly time consuming, especially for small organisms, such as Foraminifera, a group of shell-building microbial eukaryotes. To analyze large amounts of samples more efficiently, species identification methods have extended to molecular tools in the last few decades. Although a wide range of phyla have good markers available, for Foraminifera only one hypervariable marker from the ribosomal region (18S) is widely used. Recently a new mitochondrial marker cytochrome oxidase subunit 1 (COI) has been sequenced. Here we investigate whether this marker has a higher potential for species identification compared to the ribosomal marker. We explore the genetic variability of both the 18S and COI markers in 22 benthic foraminiferal morphospecies (orders Miliolida and Rotaliida). Using single-cell DNA, the genetic variability within specimens (intra) and between specimens (inter) of each species was assessed using next-generation sequencing. Amplification success rate was twice as high for COI (151/200 specimens) than for 18S (73/200 specimens). The COI marker showed greatly decreased intra- and inter-specimen variability compared to 18S in six out of seven selected species. The 18S phylogenetic reconstruction fails to adequately cluster multiple species together in contrast to COI. Additionally, the COI marker helped recognize misclassified specimens difficult to morphologically identify to the species level. Integrative taxonomy, combining morphological and molecular characteristics, provides a robust picture of the foraminiferal species diversity. Finally, we suggest the use of a set of sequences (two or more) to describe species showing intra-genomic variability additionally to using multiple markers. Our findings highlight the potential of the newly discovered mitochondrial marker for molecular species identification and metabarcoding purposes.https://www.frontiersin.org/articles/10.3389/fmars.2022.809659/fullprotisthigh-throughput sequencingmetabarcodingintra-genomic variationbenthic foraminifera |
| spellingShingle | Elsa B. Girard Elsa B. Girard Anouk Langerak Jamaluddin Jompa Owen S. Wangensteen Jan-Niklas Macher Willem Renema Willem Renema Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera Frontiers in Marine Science protist high-throughput sequencing metabarcoding intra-genomic variation benthic foraminifera |
| title | Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera |
| title_full | Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera |
| title_fullStr | Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera |
| title_full_unstemmed | Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera |
| title_short | Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera |
| title_sort | mitochondrial cytochrome oxidase subunit 1 a promising molecular marker for species identification in foraminifera |
| topic | protist high-throughput sequencing metabarcoding intra-genomic variation benthic foraminifera |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2022.809659/full |
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