ArticleProceedings of the National Academy of Sciences of the United States of America2015
Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 48 citations in OpenAlex.
- Biosynthetic origin of anticancer dolastatin 15 reveals a noncanonical NRPS architecture enabling 2-keto acid activation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Article
- VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.BMC bioinformatics · 2022Article
- Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to AssessFrontiers in microbiology · 2022Article
- Coming full circle on diazotrophy in the marine cyanobacteriumProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium.Molecular biology and evolution · 2021Article
- Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the NFrontiers in microbiology · 2019Article
- Structural and functional characterization of IdiA/FutA (Tery_3377), an iron-binding protein from the ocean diazotrophThe Journal of biological chemistry · 2018Article
- The future of genomics in polar and alpine cyanobacteria.FEMS microbiology ecology · 2018Article
- Nutrient-Colimited Trichodesmium as a Nitrogen Source or Sink in a Future Ocean.Applied and environmental microbiology · 2018Article
- Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen FixerFrontiers in microbiology · 2018Article
- Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling.Applied and environmental microbiology · 2018Article
- Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean.The ISME journal · 2017Article
- The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions.The ISME journal · 2017Article
- The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum.BMC systems biology · 2017Article
- Desert Dust as a Source of Iron to the Globally Important DiazotrophFrontiers in microbiology · 2017Article
- Microbiome ofFrontiers in microbiology · 2017Article
- Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean.Nature communications · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual "inflation" of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.
Indexed as
Identifiers
What OpenQuestion holds
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.