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

Diatoms are the most species-rich group of micro-algae, 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 T. 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.硅藻（Diatoms）是物种丰富度最高的微藻类群，其对全球海洋初级生产的贡献举足轻重。硅藻可通过快速无性繁殖形成高密度水华；水华过程中获得并传播的突变，可提供遗传乃至表型变异的基础，供自然选择作用。本研究通过对拟菱形藻属（Pseudo-nitzschia）、角毛藻属（Ditylum）与海链藻属（Thalassiosira）3个硅藻属的同源基因开展全基因组与全转录组成对比较，检验正选择信号，这3个属的系统发育距离依次递减。正选择信号在两株假微型海链藻（T. pseudonana）之间最为显著。进一步针对7株假微型海链藻开展检测，共筛选得到809个正选择候选基因，占蛋白编码基因总数的7%。相较于全基因组背景，正选择基因集显著富集孤儿基因、编码蛋白质结合结构域的基因以及转录调控因子。结合基因表达谱分析，以及对来自相似环境区域的菌株子集的正选择基因鉴定结果，研究发现正选择基因与营养限制、海表温度两类潜在选择压力存在关联。正选择基因的鉴定，为在自然种群与实验室中验证新假说提供了契机，此类假说可整合假微型海链藻的选定基因型与其对应的表型及选择压力。