BACKGROUND Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.

中文翻译：

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鞭毛藻鞭毛虫的基因组编码具有适应功能的串联重复的单外显子基因。

背景技术藻类是在海洋和淡水环境中普遍存在的生物分类浮游生物和具有重要生态意义的浮游植物。大部分鞭毛藻是光合作用的，是水生初级产品的基础。大多数分类单元是自由生活的，而有些则可以与其他生物形成共生和寄生联系。然而，对基因组数据稀缺的可用性限制了支持这些生物适应各种生态位的分子机制的知识，部分原因是它们的基因组大小估计高达250 Gbp。目前可获得的鞭毛鞭毛藻基因组数据仅限于共生菌科（特别是造礁珊瑚的共生体）和寄生谱系，它们来自基因组尺寸范围较小的分类群，而仍然缺乏来自更多自由活动物种的基因组信息。结果在这里，我们提出了两个独立于北极和南极洲的自由生活的鞭毛藻极光的二倍体基因组草图。我们发现约68％的基因组由重复序列组成，较长的末端重复序列可能会导致种内结构差异和不同的基因组大小（3.0和2.7 Gbp）。对于每个基因组，在全长转录组数据的指导下，我们预测> 50,000个高质量的蛋白质编码基因，其中约40％位于单向基因簇中，约25％由单个外显子组成。多基因组比较揭示了特异于P. glacialis的基因，以及在冷适应的鞭毛鞭毛藻中冰结合域的常见的细菌来源。结论我们的结果阐明了选择如何在复杂的基因组结构的背景下起作用，以促进局部适应。因为大多数鞭毛鞭毛藻的基因是组成型表达的，所以北极极冰杆菌通过单向串联复制单外显子基因增强了转录反应，该单外显子基因编码对于在寒冷，低光照的极地环境中生存至关重要的功能。这些基因组为将来鞭毛藻进化研究提供了基础参考。