ArticleProceedings of the National Academy of Sciences of the United States of America2012
Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Nucleosome Assembly Protein 1 in Dinoflagellate Cells Without Architectural Nucleosomes.International journal of molecular sciences · 2026Article
- RNA-Binding Proteins in Dinoflagellates.International journal of molecular sciences · 2026Review
- Collectors, not hoarders: Complex gene structures in Amphidinium carterae revealed through nanopore sequencing.BMC genomics · 2025Article
- Unraveling a Receptor-Mediated Bioluminescence Signaling Pathway in Red Tide Algae.Journal of molecular biology · 2025Article
- Review
- Phylogenetic distribution of DNA topoisomerase VI and its distinction from SPO11.NAR genomics and bioinformatics · 2024Article
- Full-length transcriptome analysis of a bloom-forming dinoflagellate Prorocentrum shikokuense (Dinophyceae).Scientific data · 2024Article
- Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates.NAR genomics and bioinformatics · 2024Article
- Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts.Open biology · 2023Article
- The enigmatic nucleus of the marine dinoflagellatemSphere · 2023Article
- The Symbiodinium Proteome Response to Thermal and Nutrient Stresses.Plant & cell physiology · 2023Article
- Strategy for the Adaptation to Stressful Conditions of the Novel Isolated Conditional Piezophilic Strain Halomonas titanicae ANRCS81.Applied and environmental microbiology · 2023Article
- Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral.PNAS nexus · 2022Article
- Orchestrated translation specializes dinoflagellate metabolism three times per day.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A Strategy for Gene Knockdown in Dinoflagellates.Microorganisms · 2022Article
- The enigmatic clock of dinoflagellates, is it unique?Frontiers in microbiology · 2022Review
- Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea.BMC genomics · 2021Article
- Assessing nucleic acid binding activity of four dinoflagellate cold shock domain proteins from Symbiodinium kawagutii and Lingulodinium polyedra.BMC molecular and cell biology · 2021Article
- Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.Nature genetics · 2021Article
- Essential components of the xanthophyll cycle differ in high and low toxin Karenia brevis.Harmful algae · 2021Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Dinoflagellates are an important component of the marine biota, but a large genome with high-copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. More importantly, little is known about the expression and conservation of these unusual gene arrays. We assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate Lingulodinium polyedrum from RNA-Seq (Illumina) reads. The catalog contains 93% of a Lingulodinium EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, indicating it is a good representation of the transcriptome. Analysis of the catalog shows a marked underrepresentation of DNA-binding proteins and DNA-binding domains compared with other algae. Despite this, we found no evidence to support the proposal of polycistronic transcription, including a marked underrepresentation of sequences corresponding to the intergenic spacers of two tandem array genes. We also have used RNA-Seq to assess the degree of sequence conservation in tandem array genes and found their transcripts to be highly conserved. Interestingly, some of the sequences in the catalog have only bacterial homologs and are potential candidates for horizontal gene transfer. These presumably were transferred as single-copy genes, and because they are now all GC-rich, any derived from AT-rich contexts must have experienced extensive mutation. Our study not only has provided the most complete dinoflagellate gene catalog known to date, it has also exploited RNA-Seq to address fundamental issues in basic transcription mechanisms and sequence conservation in these algae.
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