Poretti Manuel, Praz Coraline R, Sotiropoulos Alexandros G, Wicker Thomas
Department of Plant and Microbial Biology University of Zurich Zurich Switzerland.
Department of Biology University of Fribourg Fribourg Switzerland.
Plant Direct. 2023 Mar 16;7(3):e484. doi: 10.1002/pld3.484. eCollection 2023 Mar.
Diploid plant genomes typically contain ~35,000 genes, almost all belonging to highly conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs; however, they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in , using newly available genome assemblies of wheat, barley, and rye. Applying a set of stringent criteria, we identified 5942 candidate -specific genes (TSGs), of which 2337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in putative secreted proteins. Some were previously described to be involved in non-host resistance and cold response. Additionally, we show that 1079 TSGs have sequence homology to transposable elements (TEs), ~68% of them deriving from regulatory non-coding regions of retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that probably possess ~779 lineage-specific genes per haploid genome. TSGs, which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in . Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.
二倍体植物基因组通常包含约35000个基因，几乎所有基因都属于高度保守的基因家族。只有一小部分是谱系特异性的，仅在一个或少数几个亲缘关系密切的物种中发现。关于植物基因组中基因如何从头产生以及这种情况发生的频率知之甚少；然而，人们认为它们对于植物的多样化和适应性很重要。我们利用小麦、大麦和黑麦新获得的基因组组装数据，开发了一种流程来鉴定特定谱系的基因。应用一套严格的标准，我们鉴定出5942个候选特定谱系基因（TSGs），其中2337个在小麦中被验证为蛋白质编码基因。差异基因表达分析表明，胁迫诱导的小麦TSGs在假定的分泌蛋白中高度富集。其中一些先前被描述为参与非寄主抗性和冷反应。此外，我们表明1079个TSGs与转座元件（TEs）具有序列同源性，其中约68%来自逆转座子的调控非编码区。最重要的是，我们证明这些TSGs在跨膜结构域中富集，并且是小麦中总体表达量最高的基因之一。总之，我们得出结论，从头基因形成相对罕见，每个单倍体基因组可能拥有约779个特定谱系基因。对病原体和环境胁迫有反应的TSGs可能是未来小麦定向抗性育种的有趣候选基因。最后，我们提出TEs的非编码区可能为跨膜结构域的功能创新和新型分泌蛋白的进化提供重要的遗传原材料。
