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Estimate of the sequenced proportion of the global prokaryotic genome

Authors
  • Zhang, Zheng1, 2
  • Wang, Jianing1
  • Wang, Jinlan3
  • Wang, Jingjing1
  • Li, Yuezhong1
  • 1 Shandong University, Qingdao, 266237, China , Qingdao (China)
  • 2 Shandong University, Suzhou, 215123, China , Suzhou (China)
  • 3 Health Commission of Shandong Province, Jinan, 250014, China , Jinan (China)
Type
Published Article
Journal
Microbiome
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Sep 16, 2020
Volume
8
Issue
1
Identifiers
DOI: 10.1186/s40168-020-00903-z
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundSequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases.ResultsOur results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4–86.3%) and 18.8% (9.1–52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa.ConclusionsThese results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions.EHyGD1bcuvyriCzccWszavVideo Abstract

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