Abstract
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.
Highlights
Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization
We explore the genomic features of the pennate raphid benthic diatom Seminavis robusta to improve our understanding of genome evolution in diatoms as well as to provide insights into the molecular basis of ecological adaptations to the benthos
After removing four scaffolds corresponding to bacterial contamination (Supplementary Fig. 2), the assembly consisted of 4754 genomic scaffolds covering 125.57 Mb, which is within the range of estimated genome sizes, and had a scaffold N50 of 51 kb (Fig. 1a)
Summary
Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. Compared to the largely planktonic group of centric diatoms, the predominantly benthic and evolutionary younger pennate diatoms are far more species-rich[6] This remarkable diversification is especially pronounced among the raphid pennates, being attributed to their heterothallic mating systems and active cell motility. Motility of gametangial cells or gametes enables pheromoneguided mate finding, optimizing encounter success between opposite mating types in highly diverse and densely packed biofilms[7] Combined, these two features may underlie the extraordinary diversity of raphid diatom species with often finely differentiated abiotic and biotic microniches[2]. Through the integrative analysis of the genome sequence of S. robusta, resequencing data of additional strains, detailed gene expression profiles, and gene information of 88 other diatom species, we shed light on key genes mediating differences in cell symmetry, motility and environmental adaptations between distinct groups of diatom clades
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