Department of Geology, Lund University, Lund, Sweden.
Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
Genome Biol Evol. 2023 Dec 1;15(12). doi: 10.1093/gbe/evad212.
Numerous factors shape the evolution of protein-coding genes, including shifts in the strength or type of selection following gene duplications or changes in the environment. Diatoms and other silicifying organisms use a family of silicon transporters (SITs) to import dissolved silicon from the environment. Freshwaters contain higher silicon levels than oceans, and marine diatoms have more efficient uptake kinetics and less silicon in their cell walls, making them better competitors for a scarce resource. We compiled SITs from 37 diatom genomes to characterize shifts in selection following gene duplications and marine-freshwater transitions. A deep gene duplication, which coincided with a whole-genome duplication, gave rise to two gene lineages. One of them (SIT1-2) is present in multiple copies in most species and is known to actively import silicon. These SITs have evolved under strong purifying selection that was relaxed in freshwater taxa. Episodic diversifying selection was detected but not associated with gene duplications or habitat shifts. In contrast, genes in the second SIT lineage (SIT3) were present in just half the species, the result of multiple losses. Despite conservation of SIT3 in some lineages for the past 90-100 million years, repeated losses, relaxed selection, and low expression highlighted the dispensability of SIT3, consistent with a model of deterioration and eventual loss due to relaxed selection on SIT3 expression. The extensive but relatively balanced history of duplications and losses, together with paralog-specific expression patterns, suggest diatoms continuously balance gene dosage and expression dynamics to optimize silicon transport across major environmental gradients.
众多因素影响着蛋白质编码基因的进化，包括基因复制后选择的强度或类型的变化，以及环境的变化。硅藻和其他硅质化生物利用一系列硅转运蛋白（SITs）从环境中吸收溶解硅。淡水的硅含量高于海洋，而海洋硅藻具有更高的吸收动力学效率和细胞壁中更少的硅，这使它们成为稀缺资源的更好竞争者。我们从 37 个硅藻基因组中编译了 SITs，以描述基因复制和海洋-淡水过渡后选择的变化。一次深度基因复制与全基因组复制同时发生，产生了两个基因谱系。其中一个（SIT1-2）在大多数物种中存在多个拷贝，已知其能主动吸收硅。这些 SITs 在强烈的净化选择下进化，而在淡水分类群中这种选择被放松。我们检测到了间歇性的多样化选择，但与基因复制或栖息地变化无关。相比之下，第二个 SIT 谱系（SIT3）的基因只存在于一半的物种中，这是多次丢失的结果。尽管 SIT3 在过去的 90-100 万年中在一些谱系中保持保守，但多次丢失、选择放松和低表达突出了 SIT3 的非必需性，这与由于对 SIT3 表达的选择放松而导致其恶化和最终丢失的模型一致。大量但相对平衡的重复和丢失历史，以及等位基因特异性表达模式，表明硅藻不断平衡基因剂量和表达动力学，以优化硅质跨主要环境梯度的运输。
