Sequencing Effort Dictates Gene Discovery in Marine Microbial Metagenomes
AuthorsDuarte, Carlos M.
Pearman, John K.
Eguíluz, V. M.
Acinas, Silvia G.
Gasol, Josep M.
Bajic, Vladimir B.
KAUST DepartmentApplied Mathematics and Computational Science Program
Biological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Marine Science Program
Plankton ecology Research Group
Red Sea Research Center (RSRC)
Online Publication Date2020-09-29
Print Publication Date2020-11
Embargo End Date2021-08-03
Permanent link to this recordhttp://hdl.handle.net/10754/664543
MetadataShow full item record
AbstractMassive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of ocean and host-associated microbes. Global expeditions conducted over the past 15 years have sampled to 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 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 This article is protected by copyright. All rights reserved.
CitationDuarte, C. M., Ngugi, D. K., Alam, I., Pearman, J., Kamau, A., Eguiluz, V. M., … Irigoien, X. (2020). Sequencing Effort Dictates Gene Discovery in Marine Microbial Metagenomes. Environmental Microbiology. doi:10.1111/1462-2920.15182
CollectionsArticles; Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC); Bioscience Program; Marine Science Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
- Red Sea SAR11 and <i>Prochlorococcus</i> Single-Cell Genomes Reflect Globally Distributed Pangenomes.
- Authors: Thompson LR, Haroon MF, Shibl AA, Cahill MJ, Ngugi DK, Williams GJ, Morton JT, Knight R, Goodwin KD, Stingl U
- Issue date: 2019 Jul 1
- Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea.
- Authors: Arif M, Gauthier J, Sugier K, Iudicone D, Jaillon O, Wincker P, Peterlongo P, Madoui MA
- Issue date: 2019 Mar
- Metagenomic exploration of viruses throughout the Indian Ocean.
- Authors: Williamson SJ, Allen LZ, Lorenzi HA, Fadrosh DW, Brami D, Thiagarajan M, McCrow JP, Tovchigrechko A, Yooseph S, Venter JC
- Issue date: 2012
- Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.
- Authors: Stewart FJ, Dalsgaard T, Young CR, Thamdrup B, Revsbech NP, Ulloa O, Canfield DE, Delong EF
- Issue date: 2012
- Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound.
- Authors: Port JA, Wallace JC, Griffith WC, Faustman EM
- Issue date: 2012