ArticleExtremophiles : life under extreme conditions2014
Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.
Article in Extremophiles : life under extreme conditions, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 51 citations in OpenAlex.
- Type IV-C CRISPR-Cas effector complexes recognize double-stranded DNA and switch on collateral cleavage of ssDNA and RNA.Cell reports · 2026Article
- Chromatin and gene regulation in archaea.Molecular microbiology · 2025Review
- A virus-borne DNA damage signaling pathway controls the lysogeny-induction switch in a group of temperate pleolipoviruses.Nucleic acids research · 2023Article
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- Capillary Electrophoresis-Based Functional Genomics Screening to Discover Novel Archaeal DNA Modifying Enzymes.Applied and environmental microbiology · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Lytic archaeal viruses infect abundant primary producers in Earth's crust.Nature communications · 2021Article
- Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea.The CRISPR journal · 2020Article
- PADS Arsenal: a database of prokaryotic defense systems related genes.Nucleic acids research · 2020Article
- Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility.PLoS biology · 2019Article
- Integrated mobile genetic elements in Thaumarchaeota.Environmental microbiology · 2019Article
- Article
- Towards functional characterization of archaeal genomic dark matter.Biochemical Society transactions · 2019Review
- Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation.Nature microbiology · 2019Article
- History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology.Journal of bacteriology · 2018Review
- A novel family of tyrosine integrases encoded by the temperate pleolipovirus SNJ2.Nucleic acids research · 2018Article
- Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements.Cell reports · 2017Article
- Evolutionary Genomics of Defense Systems in Archaea and Bacteria.Annual review of microbiology · 2017Review
- 'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.Nature communications · 2017Article
- Microbial Diversity in Extreme Marine Habitats and Their Biomolecules.Microorganisms · 2017Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
Microbial genomes encompass a sizable fraction of poorly characterized, narrowly spread fast-evolving genes. Using sensitive methods for sequences comparison and protein structure prediction, we performed a detailed comparative analysis of clusters of such genes, which we denote "dark matter islands", in archaeal genomes. The dark matter islands comprise up to 20% of archaeal genomes and show remarkable heterogeneity and diversity. Nevertheless, three classes of entities are common in these genomic loci: (a) integrated viral genomes and other mobile elements; (b) defense systems, and (c) secretory and other membrane-associated systems. The dark matter islands in the genome of thermophiles and mesophiles show similar general trends of gene content, but thermophiles are substantially enriched in predicted membrane proteins whereas mesophiles have a greater proportion of recognizable mobile elements. Based on this analysis, we predict the existence of several novel groups of viruses and mobile elements, previously unnoticed variants of CRISPR-Cas immune systems, and new secretory systems that might be involved in stress response, intermicrobial conflicts and biogenesis of novel, uncharacterized membrane structures.
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Registered trials
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.