ArticleProceedings of the National Academy of Sciences of the United States of America2005
A high frequency of overlapping gene expression in compacted eukaryotic genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 104 citations in OpenAlex.
- Genome-wide comparative analysis reveals distinct evolutionary patterns of overlapping genes in prokaryotes and eukaryotes.Heredity · 2026Article
- ddOTs: A multiplexed quantitative ddPCR approach for resolving overlapping hepatitis B virus transcripts to decipher cccDNA-driven transcription.PLoS pathogens · 2026Article
- Genome Structure, Evolution, and Host Shift ofBiology · 2024Article
- Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.Nucleic acids research · 2024Article
- MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation.International journal of molecular sciences · 2024Article
- The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory.The Plant cell · 2023Article
- The chromatin organization of a chlorarachniophyte nucleomorph genome.Genome biology · 2022Article
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
- Impact of Genome Reduction in Microsporidia.Experientia supplementum (2012) · 2022Article
- Mitonuclear genomics and aging.Human genetics · 2020Review
- Nucleomorph Small RNAs in Cryptophyte and Chlorarachniophyte Algae.Genome biology and evolution · 2019Article
- Evolution and Diversity of Pre-mRNA Splicing in Highly Reduced Nucleomorph Genomes.Genome biology and evolution · 2018Article
- Bijective codon transformations show genetic code symmetries centered on cytosine's coding properties.Theory in biosciences = Theorie in den Biowissenschaften · 2018Article
- Amalga-like virus infecting Antonospora locustae, a microsporidian pathogen of grasshoppers, plus related viruses associated with other arthropods.Virus research · 2017Article
- A Recent Whole-Genome Duplication Divides Populations of a Globally Distributed Microsporidian.Molecular biology and evolution · 2016Article
- New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach.Plant molecular biology · 2016Article
- The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp.BMC genomics · 2016Article
- The Genome of Nosema sp. Isolate YNPr: A Comparative Analysis of Genome Evolution within the Nosema/Vairimorpha Clade.PloS one · 2016Article
- Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis.BMC genomics · 2015Article
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5 authors at 2 institutions in 1 country.
Funding
Abstract
The gene density of eukaryotic nuclear genomes is generally low relative to prokaryotes, but several eukaryotic lineages (many parasites or endosymbionts) have independently evolved highly compacted, gene-dense genomes. The best studied of these are the microsporidia, highly adapted fungal parasites, and the nucleomorphs, relict nuclei of endosymbiotic algae found in cryptomonads and chlorarachniophytes. These systems are now models for the effects of compaction on the form and dynamics of the nuclear genome. Here we report a large-scale investigation of gene expression from compacted eukaryotic genomes. We have conducted EST surveys of the microsporidian Antonospora locustae and nucleomorphs of the cryptomonad Guillardia theta and the chlorarachniophyte Bigelowiella natans. In all three systems we find a high frequency of mRNA molecules that encode sequence from more than one gene. There is no bias for these genes to be on the same strand, so it is unlikely that these mRNAs represent operons. Instead, compaction appears to have reduced the intergenic regions to such an extent that control elements like promoters and terminators have been forced into or beyond adjacent genes, resulting in long untranslated regions that encode other genes. Normally, transcriptional overlap can interfere with expression of a gene, but these genomes cope with high frequencies of overlap and with termination signals within expressed genes. These findings also point to serious practical difficulties in studying expression in compacted genomes, because many techniques, such as arrays or serial analysis of gene expression will be misleading.
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