The Nuclear and Mitochondrial Genomes ofAmoebophryasp. exKarlodinium veneficum

Abstract

AbstractDinoflagellates 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 three publishedAmoebophryagenomes, this genus has considerable genomic diversity. We add to the growing genomic data forAmoebophryawith an annotated genome assembly forAmoebophryasp. exKarlodinium veneficum. This species appears to translate all three 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 previousAmoebophryagenome 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 thatAmoebophryasp. exK. veneficumdoes not have a bipartite electron transport chain, unlike previously analyzedAmoebophryaspecies. This study highlights the importance of analyzing multiple genomes from highly diverse genera such asAmoebophrya.SummaryThis new long-read assembly demonstrates the remarkable diversity found withinAmoebophrya. Despite being assigned the rank of genus, the available genome assemblies indicate significant variation in gene content, AT content, genetic codes, and potentially mitochondrial biology. Furthermore, this study contributes to the expanding list of organisms that contextually translate all three canonical stop codons. Although the mechanisms underlying such a genetic code remain elusive, the relative ease of culturingAmoebophryasuggests it may be useful as a model organism for future research on this subject.