ArticleGenome biology and evolution2017
Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution.
Article in Genome biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 43 citations in OpenAlex.
- Unveiling the functional nature of retrogenes in dinoflagellates.Open biology · 2025Article
- BiP Proteins from Symbiodiniaceae: A "Shocking" Story.Microorganisms · 2024Review
- Review
- The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance.BMC genomics · 2024Article
- Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate.Genome biology · 2023Article
- Retrotransposition facilitated the establishment of a primary plastid in the thecate amoebaProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Hypothesis: Trans-splicing Generates Evolutionary Novelty in the Photosynthetic Amoeba Paulinella.Journal of phycology · 2022Article
- Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae).Journal of phycology · 2022Review
- Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions.Frontiers in plant science · 2022Article
- Multiple waves of viral invasions in Symbiodiniaceae algal genomes.Virus evolution · 2022Article
- Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium.BMC biology · 2021Article
- Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective.Marine drugs · 2020Review
- Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome.GigaScience · 2019Article
- The Genetic Basis of Toxin Biosynthesis in Dinoflagellates.Microorganisms · 2019Review
- Article
- Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates.Scientific reports · 2019Article
- Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes.Microorganisms · 2019Review
- Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.Nature communications · 2018Article
- Dinoflagellates, a Unique Lineage for Retrogene Research.Frontiers in microbiology · 2018Article
- Article
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Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene retroposition is an important mechanism of genome evolution but the role it plays in dinoflagellates, a critical player in marine ecosystems, is not known. Until recently, when the genomes of two coral-symbiotic dinoflagellate genomes, Symbiodinium kawagutii and S. minutum, were released, it has not been possible to systematically study these retrogenes. Here we examine the abundant retrogenes (∼23% of the total genes) in these species. The hallmark of retrogenes in the genome is the presence of DCCGTAGCCATTTTGGCTCAAG, a spliced leader (DinoSL) constitutively trans-spliced to the 5'-end of all nucleus-encoded mRNAs. Although the retrogenes have often lost part of the 22-nt DinoSL, the putative promoter motif from the DinoSL, TTT(T/G), is consistently retained in the upstream region of these genes, providing an explanation for the high survival rate of retrogenes in dinoflagellates. Our analysis of DinoSL sequence divergence revealed two major bursts of retroposition in the evolutionary history of Symbiodinium, occurring at ∼60 and ∼6 Ma. Reconstruction of the evolutionary trajectory of the Symbiodinium genomes mapped these 2 times to the origin and rapid radiation of this dinoflagellate lineage, respectively. GO analysis revealed differential functional enrichment of the retrogenes between the two episodes, with a broad impact on transport in the first bout and more localized influence on symbiosis-related processes such as cell adhesion in the second bout. This study provides the first evidence of large-scale retroposition as a major mechanism of genome evolution for any organism and sheds light on evolution of coral symbiosis.
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