Literature DB >> 26100932

Capturing prokaryotic dark matter genomes.

Cyrielle Gasc1, Céline Ribière2, Nicolas Parisot3, Réjane Beugnot4, Clémence Defois5, Corinne Petit-Biderre6, Delphine Boucher7, Eric Peyretaillade8, Pierre Peyret9.   

Abstract

Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.
Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Keywords:  Complete genome reconstruction; Dark matter; Metagenomics; Single-cell genomics

Mesh:

Year:  2015        PMID: 26100932     DOI: 10.1016/j.resmic.2015.06.001

Source DB:  PubMed          Journal:  Res Microbiol        ISSN: 0923-2508            Impact factor:   3.992


  7 in total

1.  Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives.

Authors:  A Maxwell Burroughs; Margaret E Glasner; Kevin P Barry; Erika A Taylor; L Aravind
Journal:  J Biol Chem       Date:  2019-05-15       Impact factor: 5.157

2.  Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert.

Authors:  Dinka Mandakovic; Jonathan Maldonado; Rodrigo Pulgar; Pablo Cabrera; Alexis Gaete; Viviana Urtuvia; Michael Seeger; Verónica Cambiazo; Mauricio González
Journal:  Extremophiles       Date:  2018-04-23       Impact factor: 2.395

Review 3.  Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.

Authors:  Cyrielle Gasc; Eric Peyretaillade; Pierre Peyret
Journal:  Nucleic Acids Res       Date:  2016-04-21       Impact factor: 16.971

4.  Survey of the green picoalga Bathycoccus genomes in the global ocean.

Authors:  Thomas Vannier; Jade Leconte; Yoann Seeleuthner; Samuel Mondy; Eric Pelletier; Jean-Marc Aury; Colomban de Vargas; Michael Sieracki; Daniele Iudicone; Daniel Vaulot; Patrick Wincker; Olivier Jaillon
Journal:  Sci Rep       Date:  2016-11-30       Impact factor: 4.379

5.  Revealing large metagenomic regions through long DNA fragment hybridization capture.

Authors:  Cyrielle Gasc; Pierre Peyret
Journal:  Microbiome       Date:  2017-03-14       Impact factor: 14.650

6.  Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea.

Authors:  Qiyun Zhu; Christopher L Dupont; Marcus B Jones; Kevin M Pham; Zhi-Dong Jiang; Herbert L DuPont; Sarah K Highlander
Journal:  Microbiome       Date:  2018-11-08       Impact factor: 14.650

Review 7.  A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.

Authors:  Tobias Andermann; Maria Fernanda Torres Jiménez; Pável Matos-Maraví; Romina Batista; José L Blanco-Pastor; A Lovisa S Gustafsson; Logan Kistler; Isabel M Liberal; Bengt Oxelman; Christine D Bacon; Alexandre Antonelli
Journal:  Front Genet       Date:  2020-02-21       Impact factor: 4.599

  7 in total

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