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Objectives <p>Dinoflagellates are important unicellular eukaryotes found in freshwater and marine ecosystems. The Family Symbiodiniaceae is well-known as symbiotic algae in various marine organisms, including many endosymbiotic species living in cnidarian cells. In contrast, the genus <i>Effrenium</i> is non-symbiotic, exhibiting traits such as resting cyst formation and heterotrophic feeding. <i>Effrenium</i> strains have been used as controls in symbiosis-related comparative studies. The only described species, <i>E. voratum</i>, is cosmopolitan, and draft genomes of three strains have been reported. However, genomic data from strains originating in temperate Japanese regions are lacking. A high-quality draft genome of an additional <i>E. voratum</i> strain will provide valuable resources for molecular biology of symbiosis and comparative genomics on local adaptation in Symbiodiniaceae.</p> Data description <p>We describe the first draft genome (version 1) of <i>E. voratum</i> strain NIES-2908, which was isolated from the coral <i>Hydnophora exesa</i> in the temperate Japanese coastal water of Goto islands, Japan. Using PacBio HiFi sequencing, the genome was assembled to a total size of 1,006 Mbp, comprising 6,051 contigs. The GC content was 50.5%, and repetitive sequences accounted for 37.9% of the genome. Gene prediction identified 54,346 protein coding genes, with 68.4% completeness based on the BUSCO alveolate dataset.</p>

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First genome sequences of the dinoflagellate Effrenium voratum strain isolated from the coral Hydnophora exesa in temperate Japanese region

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  • 发表日期：

    2025年11月3日

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  • Yuki Yoshioka,
  • Masanobu Kawachi,
  • Mayumi Kawamitsu,
  • Albert Murzabaev,
  • Noriyuki Satoh,
  • Chuya Shinzato,
  • Eiichi Shoguchi

摘要

Objectives

Dinoflagellates are important unicellular eukaryotes found in freshwater and marine ecosystems. The Family Symbiodiniaceae is well-known as symbiotic algae in various marine organisms, including many endosymbiotic species living in cnidarian cells. In contrast, the genus Effrenium is non-symbiotic, exhibiting traits such as resting cyst formation and heterotrophic feeding. Effrenium strains have been used as controls in symbiosis-related comparative studies. The only described species, E. voratum, is cosmopolitan, and draft genomes of three strains have been reported. However, genomic data from strains originating in temperate Japanese regions are lacking. A high-quality draft genome of an additional E. voratum strain will provide valuable resources for molecular biology of symbiosis and comparative genomics on local adaptation in Symbiodiniaceae.

Data description

We describe the first draft genome (version 1) of E. voratum strain NIES-2908, which was isolated from the coral Hydnophora exesa in the temperate Japanese coastal water of Goto islands, Japan. Using PacBio HiFi sequencing, the genome was assembled to a total size of 1,006 Mbp, comprising 6,051 contigs. The GC content was 50.5%, and repetitive sequences accounted for 37.9% of the genome. Gene prediction identified 54,346 protein coding genes, with 68.4% completeness based on the BUSCO alveolate dataset.