Genome characterization and expression atlas

Illumina paired-end sequencing in combination with long PacBio reads of the Seminavis robusta D6 strain, yielding 79× and 34× coverage, respectively, were used as input for genome assembly (Supplementary Table 1). A k-mer distribution analysis of the Illumina reads revealed a high level of heterozygosity (0.79%) and an estimated genome size of 117 Mb (Supplementary Fig. 1), while flow cytometry yielded an estimate of 151 Mb (standard deviation 17.65 Mb, Supplementary Note 1). Both PacBio and Illumina data were used to generate several genome assemblies and to compare the performance of different tools and integration strategies, keeping as a final assembly the one that obtained the best balance between contiguity, completeness and quality (Supplementary Table 2 and Supplementary Note 2). 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). This genome assembly was further experimentally validated through the successful amplification of 22 regions that had the expected size (Supplementary Fig. 3 and Supplementary Table 3).

Fig. 1: Genome properties for S. robusta and comparison with other sequenced diatoms.


a Summary of the S. robusta genome assembly and gene annotation statistics. b Scatter plot showing genome assembly contiguity and gene family completeness score in sequenced diatom genomes. Every dot represents a diatom genome assembly. The x axis displays the genome size in Mb, whereas the y axis represents the number of protein-coding genes. Genome assemblies are colored according to the gene family completeness score in a rainbow scale from blue to red. The size of the circle indicates the number of scaffolds in the genome assembly. c Comparative genomics analysis among diatoms and other eukaryote species. Left side of the barplot represents the age of the genes inferred through phylostratification, whereas the right side represents the duplication information. The phylogenetic relationship between diatom species is shown in a cladogram.

Repeat detection analysis revealed that 23% of the S. robusta genome assembly consists of repeats and transposable elements (Supplementary Table 4). After masking these regions, the S. robusta genome was subjected to an initial round of gene prediction and manual curation, followed by the use of newly generated expression data to improve gene models and identify additional expressed genes. Besides nuclear RNA gene prediction, resulting in 54 rRNAs, 227 tRNAs, 46 snoRNAs, and 18 snRNAs, the chloroplast and mitochondrial genomes (Supplementary Fig. 4) were also annotated, leading to a total number of 36,254 protein-coding genes and 438 RNA genes (Fig. 1a). To date, S. robusta is the diatom with the largest number of predicted protein-coding genes, of which 88% show expression support (Supplementary Fig. 5), 63% share similarity to proteins from other eukaryotes and 60% are functionally annotated. Application of a phylogeny-based horizontal gene transfer detection procedure identified 1741 genes of putative bacterial origin16. Assessing the accuracy and quality of S. robusta gene models revealed the successful recovery of 99% of core gene families conserved in Bacillariophyta (Supplementary Note 2, Supplementary Fig. 6, and Supplementary Table 5), demonstrating the higher completeness of the S. robusta gene annotation compared with other diatoms with large (>90 Mb) genomes (Fig. 1b; Supplementary Table 6).

Newly generated expression data combined with existing data (Supplementary Table 7) were used to create a large-scale gene expression atlas profiling 31 different experimental conditions. This atlas comprises a total number of 167 samples (4.2 billion Illumina reads) and covers different sexual reproduction stages, abiotic stresses, and bacterial interaction-related treatments, the latter including responses to bacterial exudates as well as N-acyl homoserine lactones (AHLs), a class of signaling molecules involved in bacterial quorum sensing. To investigate the functional significance of the S. robusta protein-coding genes, a differential expression analysis was performed, obtaining a total of 27,963 (77%) differentially expressed genes.

Gene family expansions driving adaptive evolution

In order to study gene organization and evolution, we built the PLAZA Diatoms 1.0 platform ( to identify gene families based on the protein-coding genes from 26 eukaryotic genomes, which include nine other diatoms (Supplementary Table 8). Diatoms with the largest number of protein-coding genes (S. robusta, T. oceanica, and S. acus, Fig. 1b) had overall more families and a higher proportion of species-specific families compared with diatoms with smaller genomes such as P. tricornutum (Fig. 1c; Supplementary Note 3 and Supplementary Figs. 79). We identified 594 S. robusta expanded families (Fig. 2a; Supplementary Fig. 10), driven by different duplication mechanisms (Supplementary Fig. 11), containing 9178 genes. Despite the presence of a small number of block duplicates, no evidence for a recent whole-genome duplication was found. Several S. robusta expansions include families encoding for genes involved in molecular sensing, light signaling and motility (Fig. 2b; Supplementary Note 4). For instance, we found that the single-domain voltage-gated channels (EukCatAs) and the red/far-red light-sensing phytochrome (DPH) families expanded by dispersed and tandem gene duplicates, respectively. While the EukCatAs family has been shown to modulate gliding locomotion in raphid pennate diatoms through fast Na+/Ca2+ signaling17, the DPH family may be relevant for sensing the density and stress status of biofilms18.

Fig. 2: Species-specific and shared gene family expansions in diatoms.


a Upset plot showing the intersection of gene family expansions in diatoms. Each row represents a diatom species, reporting the total number of expanded gene families within parenthesis. Black circles and vertical lines between the rows represent the intersection of expanded families between species. The barplot indicates the total gene family count in each intersection, displaying only intersections that contain at least ten gene families. Diatoms with a genome size > 90 Mb are highlighted in bold. b Examples of species-specific and shared gene family expansions in S. robusta. Each column represents a diatom species, and each row a given gene family showing expansion in S. robusta, indicating the total number of genes in S. robusta in parenthesis and matching the font color with the intersection subset in panel a. The size of the circles is proportional to the number of genes falling under the given gene family per species, whereas the color of the circles indicates if the gene family is significantly tandem-enriched. Source data are provided as a Source Data file. Numbers in superscript refer to families annotated in this Source Data file.

S. robusta displayed a remarkably high number of tandem duplicates (4594 genes), which is also observed for S. acus (5670 genes), as well as several multicellular eukaryotes (Fig. 1c). A DNA coverage analysis indicated that the vast majority (81–84%) of these tandem gene duplicates, organized in gene cluster arrays, exist as distinct copies in the S. robusta genome, and are not an artefact of the assembly procedure (Supplementary Fig. 12). Tandem duplications have been shown to play an important role in accommodating responses to external stimuli and adaptation to rapidly changing environments19, as well as generating novel expression patterns through exon shuffling20. Of the 318 expanded families in S. robusta having tandem duplicates, 69 were significantly enriched in tandem duplicates and only six of these families were shared with S. acus (Fig. 2b), revealing that tandem-mediated family expansions are largely species-specific (Supplementary Fig. 13). S. robusta tandem gene duplicates mainly consisted of leucine-rich repeat (LRR) containing proteins, cyclases, heat-shock factors, serine proteases, ubiquitin ligases, ricin B-like lectins, rhodopsins, ionotropic glutamate receptors, polyketide enzymes, and globins, all genes that may be important for the adaptive evolution of this species (Supplementary Table 9).

As 70% of S. robusta genes are part of multi-copy gene families, we evaluated potential divergence and redundancy of gene duplicates by studying their expression profiles (Supplementary Fig. 14). We observed that families with an increasing number of genes tended to display higher expression divergence than smaller families (Fig. 3a), and that families showing expression divergence are significantly enriched in eukaryote and diatom age classes. Conversely, families showing expression conservation are significantly enriched in the species-specific age class (Supplementary Fig. 15). These results indicate that globally gene duplication is associated with expression divergence and that expression divergence increases with the age of gene duplicates. However, 152 cases of diatom-specific or species-specific families showing strong expression divergence were found (Supplementary Fig. 15 and Supplementary Table 10), revealing that rapid expression evolution may also occur for specific gene functions encoded by young gene families. To determine under which conditions S. robusta’s families are expressed and in which processes they are involved, we identified families significantly enriched in upregulated genes under seven or more diverse experimental conditions (referred to as pleiotropic families) or in few specific related conditions.

Fig. 3: Expression analysis for S. robusta multi-copy gene families.


a Expression divergence trend for multi-copy S. robusta families (n = 4444 families). The y axis denotes the percentage of nodes showing expression divergence in the phylogenetic tree of the family, while the x axis represents the number of S. robusta gene copies in the family. Average expression divergence percentages are indicated by red dots. Median expression divergence values significantly higher than the median of all nodes are highlighted with a star (P-value < 0.05, Wilcoxon rank-sum test, two-sided). b Heatmap showing pleiotropic families significantly enriched in upregulated genes for more than seven different conditions. The x axis represents the different conditions/experiments, whereas the y axis reports the families. The significance of the upregulation in a certain condition for a family is shown in –log10(q-value) scale highlighted by a color gradient from gray to dark purple. Expansion and tandem enrichment of each family are highlighted in different colors on the right side of the heatmap. c Barplot showing family counts with significant condition-specific expression. The x axis represents the different conditions/experiments, whereas the y axis represents the number of families having significant expression bias for that condition. The color of the bars denotes the family age distribution. d Network showing families with significant specific expression in the three reproduction stages available. Families are represented with circles, while conditions are represented with diamonds. The color of the circles denotes the family age following the same color code as panel c. The edge’s width denotes the fraction of genes in the family that shows upregulation for the given condition, while the edge’s color represents the significance of the enrichment, following the same color code as panel b from gray to dark purple. Expansion and tandem enrichment of each family are indicated by the squares next to the gene family circles, also following the same color code as panel b. Source data are provided as a Source Data file. Numbers in superscript refer to families annotated in this Source Data file.

Eight out of the 11 pleiotropic families were expanded and/or enriched in tandem duplicates, and several encoded proteins involved in signaling (Fig. 3b), indicating a strong link between gene family evolution, tandem duplication, and S. robusta’s transcriptional response to environmental stimuli. The family that showed the highest pleiotropic signal is involved in cyclic guanosine monophosphate (cGMP) biosynthesis, which was shown to play a key role during the onset of sexual reproduction in S. robusta15 as well as Pseudo-nitzschia multistriata21. A recent study suggests that this signaling pathway might also be involved in the response to bacteria22. Our expression data corroborate these functions, but also indicate that the cGMP-related signaling may have a much broader role than previously thought, showing significant upregulation in a wide range of abiotic stresses (Fig. 3b). For a heat-shock transcription factor family (HSFs) expanded in diatoms9 and showing pleiotropic expression in S. robusta, we identified that this expansion happened through tandem duplication in several diatoms (Fig. 2b). Interestingly, the S. robusta NTF2-like tandem-enriched pleiotropic family had 19/68 copies annotated with the polyketide cyclase SnoaL-like domain. Enzymes for polyketide metabolism are absent in some protist lineages but expanded in others such as dinoflagellates and haptophytes, suggesting that the evolution of these compounds may have played an important role in their ecological success23.

Von Willebrand factor, type D domains (vWDs) are found in numerous extracellular proteins and are believed to be involved in protein multimerization. For example, several adhesive proteins contain vWDs (e.g., zonadhesin, sea star foot protein, diatom adhesive trail proteins), which are thought to be important for maturation of the adhesive into multiprotein complexes24,25. Sixty-one of the S. robusta vWD containing proteins also held the diatom-specific GDPH domain, hypothesized to be important for secreted diatom proteins with adhesive functions (e.g., motility, mucilage pads, gamete fusion)25. The identified pleiotropic tandem-enriched vWD family is highly abundant in raphid species and was significantly upregulated in ten different conditions in S. robusta, half of these related to bacterial interactions, suggesting that they might be important for bacterial recognition, motility, and adhesion. Hence, the expansion of the vWD family in S. robusta may reflect a key adaptation to highly heterogeneous benthic environments, which are inhabited by very diverse and dense bacterial populations compared with the water column.

In contrast to the wide expression of pleiotropic gene families, more than 200 families were identified showing significant enrichment for upregulation in one or a limited number of related conditions (Supplementary Note 5 and Supplementary Figs. 1619). Notably, many of these families were species or diatom-specific and responsive to either sexual reproduction, silica depletion, or bacterial interaction (Fig. 3c). Hence, the strong specific expression of these families indicates a role in these distinctive diatom traits. Diatoms are unique by having a silica cell wall and a size reduction–restitution life cycle, that for many diatoms, includes sexual reproduction5. Twenty-three out of the 42 reproduction responsive families are strongly expressed in the three profiled sexual stages (Fig. 3d). The 12 families with functional annotation encoded for proteins related to protein–protein interactions (BTB/POZ domain)26, U box ubiquitin ligases (Sel1 repeats), and potential candidates for cell–cell recognition of gametangia and/or fusion of gametes (integrins and M12B domain)27. In addition to these, the cyclin A/B family was enriched in all stages of sexual reproduction, indicating that some of these genes have a specific regulatory function during meiosis (Supplementary Fig. 19). Finally, eight of these reproduction responsive families showed a simultaneous enrichment for hydrogen peroxide responsive genes (Supplementary Fig. 16A), suggesting that reactive oxygen species signaling plays an important role during sexual reproduction.

S. robusta is found in shallow coastal habitats, often as part of subtidal biofilm communities, which can experience pronounced temperature changes. Seventy-one families showed specific expression toward bacterial interaction experiments (Fig. 3c; Supplementary Fig. 16B, C) and eight families toward high temperature (Supplementary Fig. 17). Half of these families were species-specific and/or lack functional annotation, but their strong specific expression now sheds light on the biological processes they are putatively active in. The functionally annotated bacterial interaction responsive families were involved in intracellular signaling, oxygen sensing, detoxification, oxidative stress responses, and cell adhesion. As an example, Arf GAPs can function as regulators of specialized membrane surfaces implicated in cell migration28. Together with their strong upregulation in the bacterial interaction experiments (Supplementary Fig. 16C), we suggest that the tandem duplication-driven expansion of these genes may be important for S. robusta cell adhesion and movement during biofilm formation. In contrast, the expansion by tandem duplicates of two families annotated as LRRs and ionotropic glutamate receptors (iGluRs) are relevant for S. robusta’s signaling during high-temperature acclimatization (Supplementary Fig. 17).

Intra-species gene variability and patterns of gene selection

Resequencing data from 48 different S. robusta strains, representing three genetically distinct clades sampled from a small geographic region14, was used to estimate the S. robusta pan-genome size and to validate the number of predicted protein-coding genes as well as the observed family expansions. While the core genome refers to genes present in all strains, the pan genome encompasses these core genes and dispensable ones present in only a subset of strains (Fig. 4a). We identified 1549 de novo genes absent from the reference strain and therefore estimated the S. robusta pan genome to cover 37,803 genes. Assessing the gene content diversity across all 49 S. robusta strains revealed that 28,120 (74%) genes were core while the remaining 9683 (26%) genes represented the potential dispensable fraction (Fig. 4b). From this dispensable fraction, we found 2551 (6.7%) softcore genes (present in >= 95%, but not all of the strains), indicating that the fraction of core genes probably ranges between 74–81% (Supplementary Fig. 20). Globally, the resequencing of individual S. robusta strains indicated an average gene count of 35,012 protein-coding genes, therefore confirming the number of genes identified in the reference strain (Fig. 4b). Clustering the strains by short-read DNA gene length coverage recovered the three genetically distinct clades and hybrid strains previously described14 (Fig. 4c), supporting our presence/absence variation classification and showing this strain variability is not simply an artefact of the procedure. In total, 73% of the reference tandem gene duplicates and 83% of the genes in expanded families were classified as core, indicating a strong conservation of duplicated genes in the different S. robusta strains. In fact, 13/16 families significantly enriched in core genes were expanded and/or enriched in tandem duplicates (Fig. 4d). These families are related to essential functions (e.g., light-harvesting involved in photosynthesis, metacaspases involved in proteolysis, cyclins controlling cell cycle regulation) but also encompass tandem-enriched expansions involved in signaling, including HSF, cGMP, and LRR related proteins. In contrast to these, 122/151 families significantly enriched in dispensable genes lacked functional annotation. Among the remaining annotated dispensable genes, we found telomeric proteins, which are known to undergo rapid evolution, in particular, it has been shown that gene duplicates create telomere paralogs with novel functions in telomere replication and chromosome end-protection29. The observation that 63% of the S. robusta dispensable genes in the reference genome were expressed and several of these encoded for transporters and metabolic proteins indicates this genomic variation represents transcriptionally active genes, potentially offering a template for phenotypic or physiological evolution in this diatom.

Fig. 4: S. robusta within-species variability using a gene-based pan-genome analysis.


a Representation of reference, core and pan gene size. The size of pan genome increases with each added strain up to 37,803 protein-coding genes, whereas the size of core genome diminishes to 28,120 protein-coding genes. Clade category color code refers to the population groups described in ref. 14. b Number of core and dispensable genes per S. robusta strain. The pie chart shows the total gene count, where core genes are genes present in all strains, dispensable genes are genes present in a subset of strains. c Percentage of gene length coverage by short read for all pan genes for each strain. The x axis represents the S. robusta strains, whereas the y axis represents all protein-coding pan genes. The percentage of horizontal gene coverage is highlighted by a color gradient from white (0%) to dark purple (100%). Gene categories are labeled on the right side of the y axis following the color code of panel b, whereas clade categories are labeled on the upper part of x axis following the color code of panel a. d Set of gene families that are significantly enriched in core genes. The x axis represents the percentage of protein-coding pan genes that are core or dispensable, following the color code of panel b, while the y axis represents gene families, denoting in parenthesis the total number of pan genes belonging to that gene family (reference and de novo genes). Expansion, tandem enrichment, and age of each family are highlighted in different colors on the right side of the y axis. Numbers in superscript refer to families annotated in Source Data file from Fig. 3. Source data underlying Fig. 4a, b are provided as a Source Data file.

The S. robusta dispensable gene fraction is comparable with what has been described in the marine phytoplankton E. huxleyi, where 33% of the reference genes were missing in other strains30, and plants (20–27% dispensable genes in Brassica oleracea, Helianthus annuus, Brachypodium distachyon, and Solanum lycopersicum31). However, determining the size of the dispensable gene content using resequencing data of ten geographically distant accessions in P. tricornutum32 revealed that only 4.46% of the genes are absent in at least one accession (558/12,517 core genes, 172 de novo-assembled genes). The six times higher fraction of dispensable genes in S. robusta suggests much more de novo gene evolution in this benthic diatom compared with P. tricornutum, although convergent gene loss due to long-term culturing for the latter species might provide an alternative explanation.

To evaluate conservation at the amino acid level and identify S. robusta genes that are under positive or purifying selection, we used the resequencing strains to generate a high-confidence coding single-nucleotide polymorphism (SNP) data set (see Supplementary Note 6 and Supplementary Fig. 21). The average estimates of nucleotide diversity at nonsynonymous (πN) and synonymous (πS) sites were 0.003 and 0.022, respectively. This indicates that two homologous sequences drawn at random from different strains will on average differ by 2.2% on synonymous sites and 0.3% on nonsynonymous sites. The average πNS ratio was 0.14, which is smaller than what has been reported in other organisms such as O. tauri (0.20)33, C. reinhardtii (0.22)34, or the pennate diatom P. tricornutum (0.43)32. These differences reveal that globally the analyzed amino acid composition of S. robusta genes undergoes a higher level of purifying selection, which is expected if it has a larger effective population size, as suggested by the higher πS. Furthermore, the distribution of the πNS ratio was estimated on individual genes. Interestingly, genes with higher πNS ratios, suggesting positive selection, were significantly enriched in genes upregulated during early, middle, and late sexual reproduction stages, showing that genes involved in sexual reproduction are more prone to undergo diversification in their amino acid sequence, resulting in potential new protein functions or reflecting coevolution of receptor/ligand systems. Although some of these genes belonged to pleiotropic families (e.g cGMPs and vWDs) and families with reproduction expression bias (e.g., BTB/POZ domain and U box ubiquitin ligases) discussed previously, the vast majority were, however, genes of unknown function (100/128 genes) and/or species-specific single copy (63/128), representing interesting candidates for future experimental characterization.

In addition, median πNS values were further analyzed to compare levels of purifying selection between distinct gene groups. Focusing on different gene age classes, we observed that gene age is positively correlated with purifying selection, with old genes being significantly more constrained than young genes (Supplementary Fig. 22A). Genes with homologs in other eukaryotes are also more likely to be functionally annotated than species-specific genes; hence, poorly characterized genes showed significantly less purifying selection than genes having functional annotations (Supplementary Fig. 22B). Likewise, dispensable genes had significantly higher πNS values than core genes (Supplementary Fig. 22C), suggesting reduced functional constraint for variable genes in the S. robusta species complex. Strikingly, single-copy genes did not display significantly more purifying selection than duplicated genes. In contrast, when comparing between gene duplicate types, tandem duplicates were under less constraint than dispersed duplicates (Supplementary Fig. 22D), indicating that tandem duplicates are more susceptible to amino acid changes, representing the potential evolution towards novel functionalities. We further observed that genes that are not expressed or show condition-specific expression were less constrained than genes that are broadly expressed (Supplementary Fig. 22E, F), the latter being frequently associated with housekeeping functions. Overall, our findings reveal that different levels of purifying selection act on different subsets of the S. robusta gene repertoire, and that dispensable genes as well as genes showing expression under few experimental conditions are less evolutionary constrained, suggesting they might only be relevant in specific environments.

Genes involved in cell motility and benthic adaptations

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) database35 was used as a reference data set to find S. robusta signature genes that might be implicated in specific morphological or ecological properties. These genes were identified by first determining, for each S. robusta gene, homologs in a set of 88 diatoms and subsequently selecting those genes predominantly present in pennate, raphid, and benthic species, compared with centric, araphid, and planktonic species, respectively (see “Methods”). The differential expression of these S. robusta signature genes was further inspected to give more insight into the biological roles of these genes.

A significant number of genes showing high pennate signature were downregulated during silica depletion (55/630 genes). As many of these signature genes were related to cytoskeleton and membrane composition, this suggests they might play a role in cell wall and/or pennate cell shape formation (Fig. 5a; Supplementary Note 7 and Supplementary Figs. 2328). Some examples of these cytoskeleton proteins include an actin-related protein 10 and a microtubule motor kinesin, modulating the dynein-mediated movement that contributes to nuclear migration during mitosis36. Another gene with high pennate signature encodes a tubulin–tyrosine ligase/tubulin polyglutamylase, involved in the post-translational modification of tubulins, as well as a CLASP N-terminal protein, implicated in the attachment of microtubules to the cell cortex and therefore regulating their stability. The loss-of-function mutation of the latter gene in A. thaliana has shown to result in various plant growth reductions, cell form defects, and reduced mitotic activity37, indicating that CLASP genes can potentially contribute to differences between pennate and centric diatoms in cell division and expansion. We also identified the nucleolar Las1-like protein showing high conservation in pennate diatoms, which has been linked to cell morphogenesis and cell surface growth in yeast38 and showed strong upregulation during early sexual reproduction in S. robusta. Related to membrane composition, we identified a CAAX amino terminal protease, inserted in the bilayer structure of the membrane, that is potentially implicated in protein and/or peptide modification and secretion39. The upregulation of this protease during early sexual reproduction hints toward a role in recognition during cell pairing between opposite mating types. In contrast, we found a fatty acid desaturase with high pennate signature upregulated during low temperatures, indicating that centric and pennate species might have also evolved different mechanisms to increase membrane fluidity for cold adaptation. The finding of 40 genes belonging to the CRAL-TRIO lipid binding superfamily further suggests the existence of differences in phospholipid metabolism40.

Fig. 5: Selection of signature genes showing strong clade-specific conservation.


Significant enrichment for differential expression in the S. robusta transcriptome of genes showing the specified signature is highlighted with downward (for downregulation) or upward (for upregulation) arrows colored by experiment. Each row is a protein domain, the number of genes showing the signature, and having that protein domain is indicated in parenthesis. If any of the genes containing one of the highlighted protein domains belong to an expanded and/or tandem-enriched family, this is encoded by the size and color of the circles. The fill of the circles indicates if all or some genes with a given protein domain are upregulated during bacterial interaction experiments. The average pennate/raphid/benthic signature per protein domain is highlighted by a color gradient from dark gray (−6) to dark green (6). A selection of genes with high pennate signature is shown in panel (a), which high raphid signature in panel (b) and with high benthic signature in panel (c). Source data are provided as a Source Data file.

In addition to these pennate signature genes, we also searched for raphid-specific and benthic-specific traits in the diatom phylogeny (Supplementary Fig. 29), finding proteins widely conserved in most raphid species and others more restricted to certain benthic species. In particular, within the 241 genes showing a high raphid signature, several genes related to cell adhesion and motility were found, including three proteins containing the ancient cell adhesion domain fasciclin (FAS1) and eight with a “peptidase C2, calpain” domain (Fig. 5b; Supplementary Note 7 and Supplementary Figs. 3033). Raphid species are responsive to intracellular calcium, playing a role in changing the speed and direction of locomotion41. Calpain proteins are calcium-responsive intracellular proteases that are implicated in the regulation of cell migration by controlling the dynamics of both integrin-mediated adhesion and actin-based membrane protrusion, enabling cell movement by modifying these adhesion sites42. To achieve their gliding motility and underwater adhesion, raphid diatoms secrete carbohydrate-rich extracellular polymeric substances (EPS)25. In line with this, multiple proteins with strong raphid conservation related to carbohydrate metabolism were identified, comprising one glycoside hydrolase and seven exostosin-like proteins, the latter encoding glycosyltransferases involved in the synthesis of sulphated proteoglycans present in the extracellular matrix of mammalian cells43. Interestingly, sulphated polysaccharides/proteoglycans have been identified in the EPS and cell wall-associated glycoproteins of raphid benthic diatoms, such as Stauroneis amphioxys and Craspedostauros australis44,45. The strong conservation of several of these exostosin-like proteins in different raphid benthic species (Supplementary Fig. 33) hints toward their importance for EPS synthesis in these diatoms. In addition, the presence of a raphid-specific ornithine decarboxylase, upregulated during reproduction, further suggests there are unique enzymes in raphid species controlling cell wall synthesis, since the inhibition of ornithine decarboxylase, which affects polyamine biosynthesis, has shown to result in a dramatic alteration of diatom silica structure46. Furthermore, several raphid-specific membrane transporters were found, as well as proteins containing the “Rab-GTPase-TBC”, “exocyst complex component EXOC3/Sec6”, or “target SNARE coiled-coil” domain, the latter three encoding key components related to vesicle trafficking47.

Benthic diatoms are frequently part of illuminated surfaces in shallow aquatic systems that are inhabited by dense and highly productive phototrophic biofilms, which are characterized by highly variable oxygen and light conditions. To identify genes that can be linked with molecular components explaining the success of diatoms in these environments, we explored the S. robusta gene functions showing strong conservation in other benthic diatoms. Within the set of 492 benthic signature genes, we observed a strong overrepresentation of different genes that can directly be related to oxygen and light signaling as well as diatom–bacteria interactions (Fig. 5c). Twelve globin-like S. robusta genes with high benthic signature, organized in three different families, were identified. Globins have been found across all phyla of life, meaning that the oxygen transport function of vertebrate hemoglobins is a relatively recent adaptation and that the early globin functions were enzymatic and oxygen-sensing. Dissolved and particulate carbon and nutrient levels are higher within benthic habitats compared with the water column, increasing microbial numbers and heterotrophic activity. As a result, oxygen is quickly depleted, leading to a steep redox gradient in the sediment48, which implies benthic species may have evolved mechanisms to sense oxygen concentration changes and regulate chemotaxis towards optimal conditions. One of the globin-like signature families is within the top pleiotropic families expanded by tandem duplication (Fig. 3b; Supplementary Fig. 34) and is restricted to pennate diatoms (Fig. 2b), while the other two families encode for benthic-specific globins (Supplementary Fig. 35). Whereas one of these benthic-specific families showed strong upregulation under hydrogen peroxide treatment, future experiments are needed to clarify the role of these globin-like proteins in sensing oxygen concentrations.

We identified ten putative G-protein-coupled receptor (GPCR) rhodopsin-like proteins having high benthic signature, of which seven belong to one family expanded by tandem duplication (Fig. 2b). In the ocean, the spectral composition of light becomes progressively dominated by blue–green light (400–500 nm) with increasing depth. In biofilms, differential absorption of light by phototrophs and particulate and dissolved matter can contribute to variability in the spectral composition and intensity of available photosynthetically active radiation. Hence, benthic diatoms might have expanded and/or evolved their gene repertoire for light sensing. GPCR rhodopsin-like receptors transduce extracellular signals of a wide range of stimuli including light49. The existence of homologs to bacterial proteorhodopsins in some diatoms has been suggested to represent an alternative ATP-generating pathway, especially in iron-limited regions like the Southern Ocean50. A phylogenetic analysis revealed that the tandem-enriched family containing GPCR rhodopsin-like proteins with high benthic signature is not similar to these proteorhodopsins, rather, their members are more related to rhodopsin-like proteins found in other eukaryotes (Supplementary Fig. 36A). A differential expression analysis under different light conditions51 of the GPCR rhodopsin-like protein ortholog in P. tricornutum showed that this gene is specifically upregulated under blue–green light exposure (Supplementary Fig. 36B), confirming our hypothesis that this family plays an important role in light sensing. Apart from S. robusta, Amphora and Trybionella are other diatom genera containing these globin-like and GPCR rhodopsin-like signature genes (Supplementary Fig. 29), confirming that these traits are present in different clades of benthic diatoms.

The enrichment of benthic signature genes upregulated during bacterial interaction experiments (69 genes, Supplementary Fig. 37) strongly correlates with a benthic lifestyle, where diatom–bacteria encounters are frequent due to high cell packing in biofilm communities. Secretion of EPS by benthic diatoms and their physicochemical properties are important factors driving biofilm formation, which has been shown to be strongly influenced by interaction with bacteria and/or their extracellular substances52. Here, we found one of the previously mentioned exostosin-like proteins, as well as a trichome birefringence-like protein, both potentially related to benthic EPS synthesis. In particular, the latter protein is responsible for the O-acetylation of polysaccharides in bacterial biofilm formation, suggesting O-acetylation may also play an important role in benthic diatom biofilm architecture53. Benthic signature genes also contained several NAD- or NADP-dependent oxidoreductases and detoxification enzymes (Supplementary Fig. 37), covering seven short-chain dehydrogenases/reductases (SDRs) and seven glutathione S-transferases (GSTs). While SDRs are enzymes of a great functional diversity, GSTs are often involved in the detoxification of reactive oxygen species (ROS) and xenobiotics, indicating that benthic diatoms have an evolved gene set to control ROS homeostasis and increase oxidative stress defense in biofilms54.