Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms.

底栖硅藻是浅层淡水和沿海环境的主要初级生产者，具有重要的生态功能，例如养分循环和沉积物稳定。然而，对于它们对这些高度结构化但异构环境的进化适应知之甚少。在这里，我们报告了海洋生物膜形成硅藻Seminavis robusta的参考基因组，表明基因家族的扩张占所有 36,254 个蛋白质编码基因的四分之一。串联重复在扩展特定基因功能（包括光和氧感应）方面发挥着关键作用，这可能是其适应底栖栖息地的核心。在与细菌相互作用期间差异表达的基因在其他底栖硅藻中高度保守，而许多物种特异性基因在有性生殖期间强烈上调。结合来自 48 个菌株的重新测序数据，我们的结果提供了对底栖硅藻遗传多样性和基因功能的见解。