DeMontigny Wesley, Bachvaroff Tsvetan
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD 20742, USA.
Institute for Marine and Environmental Technology, University of Maryland Center for Environmental Sciences, Baltimore, MD 21202, USA.
G3 (Bethesda). 2025 Apr 17;15(4). doi: 10.1093/g3journal/jkaf030.
Dinoflagellates are a diverse group of microplankton that include free-living, symbiotic, and parasitic species. Amoebophrya, a basal lineage of parasitic dinoflagellates, infects a variety of marine microorganisms, including harmful-bloom-forming algae. Although there are currently 3 published Amoebophrya genomes, this genus has considerable genomic diversity. We add to the growing genomic data for Amoebophrya with an annotated genome assembly for Amoebophrya sp. ex Karlodinium veneficum. This species appears to translate all 3 canonical stop codons contextually. Stop codons are present in the open reading frames of about half of the predicted gene models, including genes essential for cellular function. The in-frame stop codons are likely translated by suppressor tRNAs that were identified in the assembly. We also assembled the mitochondrial genome, which has remained elusive in the previous Amoebophrya genome assemblies. The mitochondrial genome assembly consists of many fragments with high sequence identity in the genes but low sequence identity in intergenic regions. Nuclear and mitochondrially-encoded proteins indicate that Amoebophrya sp. ex K. veneficum does not have a bipartite electron transport chain, unlike previously analyzed Amoebophrya species. This study highlights the importance of analyzing multiple genomes from highly diverse genera such as Amoebophrya.
甲藻是一类多样的微型浮游生物，包括自由生活、共生和寄生种类。阿米巴藻属（Amoebophrya）是寄生甲藻的一个基部谱系，可感染多种海洋微生物，包括形成有害藻华的藻类。尽管目前已发表了3个阿米巴藻属的基因组，但该属具有相当大的基因组多样性。我们通过对来自有毒卡尔藻（Karlodinium veneficum）的阿米巴藻（Amoebophrya sp.）进行注释基因组组装，为阿米巴藻属不断增长的基因组数据增添了内容。该物种似乎能根据上下文翻译所有3种标准终止密码子。终止密码子存在于约一半预测基因模型的开放阅读框中，包括对细胞功能至关重要的基因。框内终止密码子可能由组装过程中鉴定出的抑制性tRNA翻译。我们还组装了线粒体基因组，这在之前的阿米巴藻基因组组装中一直难以实现。线粒体基因组组装由许多片段组成，这些片段在基因中具有高序列同一性，但在基因间区域具有低序列同一性。核编码和线粒体编码的蛋白质表明，与之前分析的阿米巴藻物种不同有毒卡尔藻的阿米巴藻没有二分电子传递链。这项研究强调了分析来自阿米巴藻属等高度多样化属的多个基因组的重要性。
