TheSeminavis robustagenome provides insights into the evolutionary adaptations of benthic diatoms

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

Diurnal transcript profiling of the diatomSeminavis robustareveals adaptations to a benthic lifestyle

“…Most rhythmic protein-coding genes displayed a 24-h (92.5%) or 12-h (7.5%) periodicity, and similar to reports in other diatoms, were predominantly phasing at dusk and at night ( Figure 1C, Supplemental Data Set 2 ) (Smith et al, 2016; Ashworth et al, 2013; Goldman et al, 2019). We cross-referenced the 10,145 protein-coding genes that were not expressed during the diurnal cycle in a publicly available S. robusta expression atlas that reports on transcriptional activity during sexual reproduction, abiotic stress and diatom-bacterial interactions (Osuna-Cruz et al, 2020). More than half (5,315) of non-diurnal genes were transcriptionally active in at least one condition, although at lower expression levels than diurnally expressed genes ( Supplemental Figure 4A ).…”

“…We cross-referenced the 10,145 protein-coding genes that were not expressed during the diurnal cycle in a publicly available S. robusta expression atlas that reports on transcriptional activity during sexual reproduction, abiotic stress and diatom-bacterial interactions (Suppl. Table 2) [33]. More than half (5,315) of non-diurnal genes were transcriptionally active in at least one condition, although at lower expression levels than diurnally expressed genes (Suppl.…”

“…In culture, S. robusta cells display typical benthic behaviour, including surface attachment, biofilm formation and vigorous gliding motility, which has been exploited to study chemotaxis [31]. Cultures from strain 85A have been popular for transcriptomics experiments [32,33,34,35]. This strain is a fifth generation lineage from the S. robusta laboratory pedigree whose ancestral clones originate from subtidal sediments of the Veerse Meer in The Netherlands (51°32'36" N, 3°48'15" E) [36,37].…”

“…Furthermore, S. robusta responds to high irradiances both by downwards migration into the sediment and the expression of photoprotective LHCX genes [40,41]. The recent generation of a reference genome assembly and the construction of a transcriptome atlas that spans various environmental conditions, biotic interactions and life cycle stages represents an important resource for comparative genomic studies, allowing to identify genomic features associated with the lifestyle of obligate benthic diatoms [33].…”

An optimised method for intact nuclei isolation from diatoms

“…Diatoms can be divided into three groups based on the ultrastructure of their cell wall: Coscinodiscophyceae (radial centrics), which show radial symmetry; Mediophyceae (including Thalassiosirales), which exhibit polar symmetry, and Bacillariophyceae (pennates), which show bilateral symmetry [6][7][8] . In the last decades, several centric and pennate diatom genomes have been released [9][10][11][12][13][14] offering a unique opportunity to investigate diatom genomic organization and function. The huge gain of knowledge brought by diatom sequenced genomes has been complemented by the development of advanced molecular tools such as stable genetic transformation through biolistic bombardment 15 and genome editing techniques 16,17 .…”