Please use this identifier to cite or link to this item:
Files in This Item:
There are no files associated with this item.
Title: Sequencing effort dictates gene discovery in marine microbial metagenomes
Authors: Duarte, Carlos M.; Ngugi, David K.; Alam, Intikhab; Pearman, John; Kamau, Allan; Eguiluz, Victor M.; Gojobori, Takashi and Acinas, Silvia G.; Gasol, Josep M.; Bajic, Vladimir; Irigoien, Xabier
Citation: ENVIRONMENTAL MICROBIOLOGY, 2020, 22, 4589-4603
Abstract: Massive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of the ocean and host-associated microbes. Global expeditions conducted over the past 15 years have sampled the ocean to build a catalogue of genes from pelagic microbes. Here we undertook a large sequencing effort of a perturbed Red Sea plankton community to uncover that the rate of gene discovery increases continuously with sequencing effort, with no indication that the retrieved 2.83 million non-redundant (complete) genes predicted from the experiment represented a nearly complete inventory of the genes present in the sampled community (i.e., no evidence of saturation). The underlying reason is the Pareto-like distribution of the abundance of genes in the plankton community, resulting in a very long tail of millions of genes present at remarkably low abundances, which can only be retrieved through massive sequencing. Microbial metagenomic projects retrieve a variable number of unique genes per Tera base-pair (Tbp), with a median value of 14.7 million unique genes per Tbp sequenced across projects. The increase in the rate of gene discovery in microbial metagenomes with sequencing effort implies that there is ample room for new gene discovery in further ocean and holobiont sequencing studies.
Issue Date: 2020
Publisher: WILEY
Type: Article
DOI: 10.1111/1462-2920.15182
ISSN: 1462-2912
E-ISSN: 1462-2920
Funder: King Abdullah University of Science and TechnologyKing Abdullah University of Science \& Technology
Malaspina 2010 Expedition Project - Spanish Ministry of Science and Innovation [CSD2008-00077]
National Institutes of HealthUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USA [AA123456, BB123456]
Appears in Publication types:Artículos científicos

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.