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Sequencing effort dictates gene discovery in marine microbial metagenomes |
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| Authors: | Carlos M Duarte David K Ngugi Intikhab Alam John Pearman Allan Kamau Victor M Eguiluz Takashi Gojobori Silvia G Acinas Josep M Gasol Vladimir Bajic Xabier Irigoien |
| Institution: | 1. King Abdullah University of Science and Technology (KAUST), Red Sea Research Centre (RSRC), Thuwal, 23955-6900 Saudi Arabia;2. King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia, Thuwal, 23955-6900 Saudi Arabia
These authors contributed equally to this work.;3. Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany;4. Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), E07122, Palma de Mallorca, Spain;5. Institut de Ciències del Mar, CSIC, Barcelona, Spain;6. Institut de Ciències del Mar, CSIC, Barcelona, Spain Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Australia;7. King Abdullah University of Science and Technology (KAUST), Red Sea Research Centre (RSRC), Thuwal, 23955-6900 Saudi Arabia AZTI – Marine Research, Herrera Kaia, Portualdea z/g, Pasaia (Gipuzkoa), 20110 Spain |
| 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. |
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