Positive selection within a diatom species acts on putative protein interactions and transcriptional regulation

Abstract

Diatoms are the most species-rich group of microalgae, and their contribution to marine primary production is important on a global scale. Diatoms can form dense blooms through rapid asexual reproduction; mutations acquired and propagated during blooms likely provide the genetic, and thus phenotypic, variability upon which natural selection may act. Positive selection was tested using genome and transcriptome-wide pair-wise comparisons of homologs in three genera of diatoms (Pseudo-nitzschia, Ditylum, and Thalassiosira) that represent decreasing phylogenetic distances. The signal of positive selection was greatest between two strains of Thalassiosira pseudonana. Further testing among seven strains of T. pseudonana yielded 809 candidate genes of positive selection, which are 7% of the protein-coding genes. Orphan genes and genes encoding protein-binding domains and transcriptional regulators were enriched within the set of positively selected genes relative to the genome as a whole. Positively selected genes were linked to the potential selective pressures of nutrient limitation and sea surface temperature based on analysis of gene expression profiles and identification of positively selected genes in subsets of strains from locations with similar environmental conditions. The identification of positively selected genes presents an opportunity to test new hypotheses in natural populations and the laboratory that integrate selected genotypes in T. pseudonana with their associated phenotypes and selective forces.

Fig. 1.

Frequency distributions of the d_N:d_S of homologs between diatom pairs for genes that are not saturated for silent substitutions (i.e., for genes where d_S < 1.0). Number of genes analyzed is in parentheses.

Fig. 2.

Boxplots and statistics of the expression of positively selected (gray) and neutral and purified (white) genes of Thalassiosira pseudonana (CCMP1335) grown in a nutrient replete control (ctrl), nutrient limitation (Si, Fe, NO₃, and CO₂), and a 4°C cold treatment. Boxplots: box = 1st and 3rd quartiles, whiskers = 1.5 × interquartile range, notch = median of expression as log₁₀(median aggregated probe intensity per gene). Mann–Whitney tests (N = 636 selected genes, N = 8,357 neutral and purified genes; *significance at P ≪ 0.01).

Fig. 3.

Relative expression for 636 of 809 positively selected genes in Thalassiosira pseudonana (CCMP1335) grown under nutrient limitation (Si, Fe, NO₃, and CO₂), a nutrient replete control, and a 4°C cold treatment. Each gene is represented by one row in the heatmap. The similarity relationship of gene expression is represented by the dendrogram to the left. The upper dendrogram represents the similarity of responses among treatments. (A) Genes associated with sexual reproduction. (B) Putative cell wall-associated genes detailed in figure 4. Data are from Mock et al. 2008; log₁₀(median aggregated probe intensity per gene) is plotted.

Fig. 4.

Relative expression and annotations of five coexpressed putative cell wall-associated genes that are positively selected in Thalassiosira pseudonana. Table headers: SP, signal peptide; T, target of peptide; DE, differentially expressed relative to control in Mock et al. (2008). Within table: Y, yes; S, secretory pathway; TF, transcription factor; PP, protein–protein interacting; TM, transmembrane region. The scale is log₁₀(median aggregated probe intensity per gene).