A metagenomic assessment of microbial eukaryotic diversity in the global ocean
14 pages, 5 figures, 1 table, supporting information https://doi.org/10.1111/1755-0998.13147.-- Data availability statement eukaryotesV4 database. Available at https://github.com/aleixop/eukaryotesV4 with https://doi.org/10.5281/zenodo.3522173. Data processing, analysis scripts, mTags and ASV tables. Available at https://github.com/aleixop/Malaspina_Euk_mTags with https://doi.org/10.5281/zenodo.3629394. Fasta files with retrieved mTags and contigs. Available at https://github.com/aleixop/Malaspina_Euk_mTags with https://doi.org/10.5281/zenodo.3629394. V4 amplicon sequences. Deposited at European Nucleotide Archive, accession number PRJEB23771, from a previous study (Giner et al., 2020). V9 amplicon sequences. Deposited at European Nucleotide Archive, under accession number PRJEB36469
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Other Authors: | |
| Format: | artículo biblioteca |
| Published: |
Wiley-Blackwell
2020-05
|
| Subjects: | Amplicon sequencing, Diversity, Global ocean, Marine protists, Metagenomics, |
| Online Access: | http://hdl.handle.net/10261/210468 http://dx.doi.org/10.13039/501100004052 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100011033 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| id |
dig-icm-es-10261-210468 |
|---|---|
| record_format |
koha |
| institution |
ICM ES |
| collection |
DSpace |
| country |
España |
| countrycode |
ES |
| component |
Bibliográfico |
| access |
En linea |
| databasecode |
dig-icm-es |
| tag |
biblioteca |
| region |
Europa del Sur |
| libraryname |
Biblioteca del ICM España |
| topic |
Amplicon sequencing Diversity Global ocean Marine protists Metagenomics Amplicon sequencing Diversity Global ocean Marine protists Metagenomics |
| spellingShingle |
Amplicon sequencing Diversity Global ocean Marine protists Metagenomics Amplicon sequencing Diversity Global ocean Marine protists Metagenomics Obiol, Aleix Rodríguez Giner, Caterina Sánchez, Pablo Duarte, Carlos M. Acinas, Silvia G. Massana, Ramon A metagenomic assessment of microbial eukaryotic diversity in the global ocean |
| description |
14 pages, 5 figures, 1 table, supporting information https://doi.org/10.1111/1755-0998.13147.-- Data availability statement eukaryotesV4 database. Available at https://github.com/aleixop/eukaryotesV4 with https://doi.org/10.5281/zenodo.3522173. Data processing, analysis scripts, mTags and ASV tables. Available at https://github.com/aleixop/Malaspina_Euk_mTags with https://doi.org/10.5281/zenodo.3629394. Fasta files with retrieved mTags and contigs. Available at https://github.com/aleixop/Malaspina_Euk_mTags with https://doi.org/10.5281/zenodo.3629394. V4 amplicon sequences. Deposited at European Nucleotide Archive, accession number PRJEB23771, from a previous study (Giner et al., 2020). V9 amplicon sequences. Deposited at European Nucleotide Archive, under accession number PRJEB36469 |
| author2 |
Ministerio de Economía y Competitividad (España) |
| author_facet |
Ministerio de Economía y Competitividad (España) Obiol, Aleix Rodríguez Giner, Caterina Sánchez, Pablo Duarte, Carlos M. Acinas, Silvia G. Massana, Ramon |
| format |
artículo |
| topic_facet |
Amplicon sequencing Diversity Global ocean Marine protists Metagenomics |
| author |
Obiol, Aleix Rodríguez Giner, Caterina Sánchez, Pablo Duarte, Carlos M. Acinas, Silvia G. Massana, Ramon |
| author_sort |
Obiol, Aleix |
| title |
A metagenomic assessment of microbial eukaryotic diversity in the global ocean |
| title_short |
A metagenomic assessment of microbial eukaryotic diversity in the global ocean |
| title_full |
A metagenomic assessment of microbial eukaryotic diversity in the global ocean |
| title_fullStr |
A metagenomic assessment of microbial eukaryotic diversity in the global ocean |
| title_full_unstemmed |
A metagenomic assessment of microbial eukaryotic diversity in the global ocean |
| title_sort |
metagenomic assessment of microbial eukaryotic diversity in the global ocean |
| publisher |
Wiley-Blackwell |
| publishDate |
2020-05 |
| url |
http://hdl.handle.net/10261/210468 http://dx.doi.org/10.13039/501100004052 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100011033 |
| work_keys_str_mv |
AT obiolaleix ametagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT rodriguezginercaterina ametagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT sanchezpablo ametagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT duartecarlosm ametagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT acinassilviag ametagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT massanaramon ametagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT obiolaleix metagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT rodriguezginercaterina metagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT sanchezpablo metagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT duartecarlosm metagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT acinassilviag metagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean AT massanaramon metagenomicassessmentofmicrobialeukaryoticdiversityintheglobalocean |
| _version_ |
1777667190907994112 |
| spelling |
dig-icm-es-10261-2104682021-05-21T07:42:26Z A metagenomic assessment of microbial eukaryotic diversity in the global ocean Obiol, Aleix Rodríguez Giner, Caterina Sánchez, Pablo Duarte, Carlos M. Acinas, Silvia G. Massana, Ramon Ministerio de Economía y Competitividad (España) King Abdullah University of Science and Technology Agencia Estatal de Investigación (España) Amplicon sequencing Diversity Global ocean Marine protists Metagenomics 14 pages, 5 figures, 1 table, supporting information https://doi.org/10.1111/1755-0998.13147.-- Data availability statement eukaryotesV4 database. Available at https://github.com/aleixop/eukaryotesV4 with https://doi.org/10.5281/zenodo.3522173. Data processing, analysis scripts, mTags and ASV tables. Available at https://github.com/aleixop/Malaspina_Euk_mTags with https://doi.org/10.5281/zenodo.3629394. Fasta files with retrieved mTags and contigs. Available at https://github.com/aleixop/Malaspina_Euk_mTags with https://doi.org/10.5281/zenodo.3629394. V4 amplicon sequences. Deposited at European Nucleotide Archive, accession number PRJEB23771, from a previous study (Giner et al., 2020). V9 amplicon sequences. Deposited at European Nucleotide Archive, under accession number PRJEB36469 This is the pre-peer reviewed version of the following article: A metagenomic assessment of microbial eukaryotic diversity in the global ocean, A. Obiol, C.R. Giner, P.Sánchez, C.M. Duarte, S.G. Acinas, R. Massana, Molecular Ecology Resources 20(3): 718-731 (2020), which has been published in final form at https://doi.org/10.1111/1755-0998.13147. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions Surveying microbial diversity and function is accomplished by combining complementary molecular tools. Among them, metagenomics is a PCR free approach that contains all genetic information from microbial assemblages and is today performed at a relatively large scale and reasonable cost, mostly based on very short reads. Here, we investigated the potential of metagenomics to provide taxonomic reports of marine microbial eukaryotes. We prepared a curated database with reference sequences of the V4 region of 18S rDNA clustered at 97% similarity and used this database to extract and classify metagenomic reads. More than half of them were unambiguously affiliated to a unique reference whilst the rest could be assigned to a given taxonomic group. The overall diversity reported by metagenomics was similar to that obtained by amplicon sequencing of the V4 and V9 regions of the 18S rRNA gene, although either one or both of these amplicon surveys performed poorly for groups like Excavata, Amoebozoa, Fungi and Haptophyta. We then studied the diversity of picoeukaryotes and nanoeukaryotes using 91 metagenomes from surface down to bathypelagic layers in different oceans, unveiling a clear taxonomic separation between size fractions and depth layers. Finally, we retrieved long rDNA sequences from assembled metagenomes that improved phylogenetic reconstructions of particular groups. Overall, this study shows metagenomics as an excellent resource for taxonomic exploration of marine microbial eukaryotes his research was supported by the Spanish Ministry of Economy and Competitiveness projects Malaspina‐2010 (CSD2008–00077) and ALLFLAGS (CTM2016‐75083‐R) and King Abdullah University of Science and Technology (KAUST) under contract OSR #3362. AO was supported by a Spanish FPI grant With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI) Peer Reviewed 2020-05-05T11:18:11Z 2020-05-05T11:18:11Z 2020-05 2020-05-05T11:18:11Z artículo http://purl.org/coar/resource_type/c_6501 issn: 1755-098X e-issn: 1755-0998 Molecular Ecology Resources 20(3): 718-731 (2020) CEX2019-000928-S http://hdl.handle.net/10261/210468 10.1111/1755-0998.13147 http://dx.doi.org/10.13039/501100004052 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100011033 #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CTM2016-75083-R https://doi.org/10.1111/1755-0998.13147 Sí open Wiley-Blackwell |