Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach
International audience Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to D...
Published in: | PLoS ONE |
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Main Authors: | , , , , |
Other Authors: | , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2014
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Subjects: | |
Online Access: | https://hal.sorbonne-universite.fr/hal-01100874 https://hal.sorbonne-universite.fr/hal-01100874/document https://hal.sorbonne-universite.fr/hal-01100874/file/Nanjappa_2014_Assessment_of.pdf https://doi.org/10.1371/journal.pone.0103810 |
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English |
topic |
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BID]Life Sciences [q-bio]/Biodiversity |
spellingShingle |
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BID]Life Sciences [q-bio]/Biodiversity Nanjappa, Deepak Audic, Stéphane Romac, Sarah Kooistra, Wiebe H.C.F. Zingone, Adriana Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
topic_facet |
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BID]Life Sciences [q-bio]/Biodiversity |
description |
International audience Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family. Methodology/Principal Findings: We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay. Conclusions/Significance: Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the ... |
author2 |
Stazione Zoologica Anton Dohrn (SZN) Evolution des Protistes et Ecosystèmes Pélagiques (EPEP) Adaptation et diversité en milieu marin (AD2M) Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) |
format |
Article in Journal/Newspaper |
author |
Nanjappa, Deepak Audic, Stéphane Romac, Sarah Kooistra, Wiebe H.C.F. Zingone, Adriana |
author_facet |
Nanjappa, Deepak Audic, Stéphane Romac, Sarah Kooistra, Wiebe H.C.F. Zingone, Adriana |
author_sort |
Nanjappa, Deepak |
title |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_short |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_full |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_fullStr |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_full_unstemmed |
Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach |
title_sort |
assessment of species diversity and distribution of an ancient diatom lineage using a dna metabarcoding approach |
publisher |
HAL CCSD |
publishDate |
2014 |
url |
https://hal.sorbonne-universite.fr/hal-01100874 https://hal.sorbonne-universite.fr/hal-01100874/document https://hal.sorbonne-universite.fr/hal-01100874/file/Nanjappa_2014_Assessment_of.pdf https://doi.org/10.1371/journal.pone.0103810 |
geographic |
Baffin Bay |
geographic_facet |
Baffin Bay |
genre |
Baffin Bay Baffin Bay Baffin North Atlantic |
genre_facet |
Baffin Bay Baffin Bay Baffin North Atlantic |
op_source |
ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.sorbonne-universite.fr/hal-01100874 PLoS ONE, Public Library of Science, 2014, 9 (8), pp.e103810. ⟨10.1371/journal.pone.0103810⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0103810 hal-01100874 https://hal.sorbonne-universite.fr/hal-01100874 https://hal.sorbonne-universite.fr/hal-01100874/document https://hal.sorbonne-universite.fr/hal-01100874/file/Nanjappa_2014_Assessment_of.pdf doi:10.1371/journal.pone.0103810 |
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info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1371/journal.pone.0103810 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
8 |
container_start_page |
e103810 |
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1766365420518899712 |
spelling |
ftccsdartic:oai:HAL:hal-01100874v1 2023-05-15T15:35:07+02:00 Assessment of Species Diversity and Distribution of an Ancient Diatom Lineage Using a DNA Metabarcoding Approach Nanjappa, Deepak Audic, Stéphane Romac, Sarah Kooistra, Wiebe H.C.F. Zingone, Adriana Stazione Zoologica Anton Dohrn (SZN) Evolution des Protistes et Ecosystèmes Pélagiques (EPEP) Adaptation et diversité en milieu marin (AD2M) Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) 2014-08-18 https://hal.sorbonne-universite.fr/hal-01100874 https://hal.sorbonne-universite.fr/hal-01100874/document https://hal.sorbonne-universite.fr/hal-01100874/file/Nanjappa_2014_Assessment_of.pdf https://doi.org/10.1371/journal.pone.0103810 en eng HAL CCSD Public Library of Science info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0103810 hal-01100874 https://hal.sorbonne-universite.fr/hal-01100874 https://hal.sorbonne-universite.fr/hal-01100874/document https://hal.sorbonne-universite.fr/hal-01100874/file/Nanjappa_2014_Assessment_of.pdf doi:10.1371/journal.pone.0103810 info:eu-repo/semantics/OpenAccess ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.sorbonne-universite.fr/hal-01100874 PLoS ONE, Public Library of Science, 2014, 9 (8), pp.e103810. ⟨10.1371/journal.pone.0103810⟩ [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] [SDV.BID]Life Sciences [q-bio]/Biodiversity info:eu-repo/semantics/article Journal articles 2014 ftccsdartic https://doi.org/10.1371/journal.pone.0103810 2021-09-04T23:20:13Z International audience Background: Continuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family. Methodology/Principal Findings: We analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay. Conclusions/Significance: Identification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the ... Article in Journal/Newspaper Baffin Bay Baffin Bay Baffin North Atlantic Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Baffin Bay PLoS ONE 9 8 e103810 |