Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis

Single-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear how useful...

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Autores: López Escardó, David, 1988-, Grau Bové, Xavier, Guillaumet-Adkins, Amy, Gut, Marta, Sieracki, Michael E., Ruiz Trillo, Iñaki
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/35162
Acceso en línea:http://hdl.handle.net/10230/35162
http://dx.doi.org/10.1038/s41598-017-11466-9
Access Level:acceso abierto
Palabra clave:Evolutionary genetics
Single-cell amplified genomes
Choanoflagellate
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dc.title.none.fl_str_mv Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
title Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
spellingShingle Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
López Escardó, David, 1988-
Evolutionary genetics
Single-cell amplified genomes
Choanoflagellate
title_short Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
title_full Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
title_fullStr Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
title_full_unstemmed Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
title_sort Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
dc.creator.none.fl_str_mv López Escardó, David, 1988-
Grau Bové, Xavier
Guillaumet-Adkins, Amy
Gut, Marta
Sieracki, Michael E.
Ruiz Trillo, Iñaki
author López Escardó, David, 1988-
author_facet López Escardó, David, 1988-
Grau Bové, Xavier
Guillaumet-Adkins, Amy
Gut, Marta
Sieracki, Michael E.
Ruiz Trillo, Iñaki
author_role author
author2 Grau Bové, Xavier
Guillaumet-Adkins, Amy
Gut, Marta
Sieracki, Michael E.
Ruiz Trillo, Iñaki
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Evolutionary genetics
Single-cell amplified genomes
Choanoflagellate
topic Evolutionary genetics
Single-cell amplified genomes
Choanoflagellate
description Single-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear how useful can SCG be to address evolutionary questions on uncultured microbial eukaryotes. To provide some insights into this, we here analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known. Our results show that each SAG has a different, independent bias, yielding different levels of genome recovery for each cell (6-36%). Genes often appear fragmented and are split into more genes during annotation. Thus, analyses of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed with a single SAG. However, the recovery of phylogenetically-informative protein domains can be up to 55%. This means SAG data can be used to perform accurate phylogenomic analyses. Finally, we also confirm that the co-assembly of several SAGs improves the general genomic recovery. Overall, our data show that, besides important current limitations, SAGs can still provide interesting and novel insights from poorly-known, uncultured organisms.
publishDate 2017
dc.date.none.fl_str_mv 2017
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/35162
http://dx.doi.org/10.1038/s41598-017-11466-9
url http://hdl.handle.net/10230/35162
http://dx.doi.org/10.1038/s41598-017-11466-9
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Scientific Reports. 2017 Sep 8;7(1):11025
info:eu-repo/grantAgreement/EC/FP7/616960
info:eu-repo/grantAgreement/ES/1PE/BFU2014-57779-P
info:eu-repo/grantAgreement/EC/FP7/287589
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
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spelling Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollisLópez Escardó, David, 1988-Grau Bové, XavierGuillaumet-Adkins, AmyGut, MartaSieracki, Michael E.Ruiz Trillo, IñakiEvolutionary geneticsSingle-cell amplified genomesChoanoflagellateSingle-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear how useful can SCG be to address evolutionary questions on uncultured microbial eukaryotes. To provide some insights into this, we here analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known. Our results show that each SAG has a different, independent bias, yielding different levels of genome recovery for each cell (6-36%). Genes often appear fragmented and are split into more genes during annotation. Thus, analyses of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed with a single SAG. However, the recovery of phylogenetically-informative protein domains can be up to 55%. This means SAG data can be used to perform accurate phylogenomic analyses. Finally, we also confirm that the co-assembly of several SAGs improves the general genomic recovery. Overall, our data show that, besides important current limitations, SAGs can still provide interesting and novel insights from poorly-known, uncultured organisms.We acknowledge support by ICREA, a European Research Council Consolidator (ERC-2012-Co-616960) grant, and grant (BFU2014-57779-P) from Ministerio de Economía y Competitividad (MINECO) with FEDER funds. We also acknowledge financial support from Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya (Project 2014 SGR 619). The authors want to acknowledge Jean-Francois Mangot for the support on the tetranucleotide frequency calculations and Ramon Massana for helpful discussions on the manuscript. We also thank Javier del Campo for some initial ideas, further discussions, and help in the experimental design. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. We also thank the commitment of the following people and sponsors: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEAthe French Government 'Investissements d'Avenir' programmes OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, and European Union FP7 (MicroB3/No.287589), We also thank the support and commitment of Agnès B. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the Eléctricité de France (EDF) Foundation, Fondation pour la recherche sur la biodiversité (FRB), the Foundation Prince Albert II de Monaco, the Tara Foundation, its schooner and teams. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who graciously granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org/en/m/science/labs-involved/).Nature Publishing Group201820182017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/35162http://dx.doi.org/10.1038/s41598-017-11466-9reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésScientific Reports. 2017 Sep 8;7(1):11025info:eu-repo/grantAgreement/EC/FP7/616960info:eu-repo/grantAgreement/ES/1PE/BFU2014-57779-Pinfo:eu-repo/grantAgreement/EC/FP7/287589© The Author(s) 2017. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/351622026-06-12T07:21:37Z
score 15.812429

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