ArticleGenome biology2007
Prediction of effective genome size in metagenomic samples.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers, 1 of them a synthesis that pooled it.
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Who cites it
149 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.PLoS computational biology · 2009Pooled it
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- Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.mSystems · 2026Article
- Soil Nutrient Enrichment Induces Trade-Offs in Bacterial Life-History Strategies Promoting Plant Productivity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Effects of vitamin BApplied and environmental microbiology · 2025Article
- Towards AI-designed genomes using a variational autoencoder.Proceedings. Biological sciences · 2024Article
- Identification of novel broad host-range promoter sequences functional in diverse Pseudomonadota by a promoter-trap approach.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Ligand cross-feeding resolves bacterial vitamin BNature · 2024Article
- Lineage-specific evolution ofApplied and environmental microbiology · 2024Article
- Quantifying microbial DNA in metagenomes improves microbial trait estimation.ISME communications · 2024Article
- DNA sequencing at the picogram level to investigate life on Mars and Earth.Scientific reports · 2023Article
- Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains.Scientific reports · 2023Article
- Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- The overlooked role of a biotin precursor for marine bacteria - desthiobiotin as an escape route for biotin auxotrophy.The ISME journal · 2022Article
- Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions.The ISME journal · 2021Article
- Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity.mSystems · 2021Article
- A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy.Frontiers in microbiology · 2021Review
- Variation in genomic traits of microbial communities among ecosystems.FEMS microbes · 2021Article
- Genome size evolution: towards new model systems for old questions.Proceedings. Biological sciences · 2020Article
- A comprehensive survey of integron-associated genes present in metagenomes.BMC genomics · 2020Article
89 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.