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.

Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 • C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment.Genes 2020, 11, 9 2 of 25 (3) both of the above, as plasticity can be adaptive with respect to a function and may be altered by natural selection and ultimately become or facilitate adaptation.In addition to natural environmental variability, diatoms used in experimental research are also exposed to another source of variability; they are removed from their natural environment, isolated and transferred to laboratory conditions in which evolutionary processes do not cease to occur [8]. Many cases of novel genetic variation have been shown after years of maintenance in culture collection [9][10][11]. Considering the high adaptability of diatoms, it could be hard to interpret the intra-specific algal diversity observed in related studies as the result of (a) adaptation to the natural environment from which strains were isolated or (b) evolutionary changes while being in culture.Temperature is a very significant environmental variable that affects the physiological response of diatoms and ultimately determines their phenological patterns and geographic ranges [12][13][14], as well as one of the parameters that is usually kept constant in culture conditions. An increase in temperature leads to an increase in enzyme activity in metabolic processes, including photosynthesis and respiration, so the cells are expected to grow faster. Even algae obtained from cold habitats have shown at least short-term temperature optima for photosynthesis several degrees higher than the temperature at which they were growing. Low temperatures lead to the exact opposite direction so that, in order to survive, cells respond with an increase in enzyme synthesis [15,16]. A recent study ...

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 resequencing data from 48 strains, our results offer new insights on the genetic diversity and gene functions in benthic diatoms.

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