MicroRNAs (miRNAs) play roles in various biological processes in plants including growth, development, and disease resistance. Previous studies revealed that some plant miRNAs produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs), and they regulate a cascade of gene expression. We performed a genome-wide comparative analysis of miRNAs in Solanaceous species (pepper, tomato, and potato), from an evolutionary perspective. Microsynteny of miRNAs was analysed based on the genomic loci and their flanking genes and most of the well-conserved miRNA genes maintained microsynteny in Solanaceae. We identified target genes of the miRNAs via degradome analysis and found that several miRNAs target many genes encoding nucleotide-binding leucine-rich repeat (NLR) or receptor-like proteins (RLPs), which are known to be major players in defense responses. In addition, disease-resistance-associated miRNAs trigger phasiRNA production in pepper, indicating amplification of the regulation of disease-resistance gene families. Among these, miR-n033a-3p, whose target NLRs have been duplicated in pepper, targets more NLRs belonging to specific subgroup in pepper than those in potato. miRNAs targeting resistance genes might have evolved to regulate numerous targets in Solanaceae, following expansion of target resistance genes. This study provides an insight into evolutionary relationship between miRNAs and their target defense genes in plants.

中文翻译：

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茄科物种的全基因组比较分析揭示了针对辣椒属中防御基因的microRNA的进化。

微小RNA（miRNA）在植物的各种生物学过程中起作用，包括生长，发育和抗病性。先前的研究表明，某些植物miRNA会产生次级小干扰RNA（siRNA），例如分阶段的次级siRNA（phasiRNA），它们调节基因表达的级联。从进化的角度，我们对茄科物种（辣椒，番茄和马铃薯）中的miRNA进行了全基因组比较分析。基于基因组位点及其侧翼基因分析了miRNA的微同义性，大多数保存良好的miRNA基因在茄科中维持了微同义性。我们通过降解分析确定了miRNA的靶基因，发现几种miRNA靶向许多编码核苷酸结合亮氨酸富集重复序列（NLR）或受体样蛋白（RLP）的基因，众所周知，它们是国防反应中的主要角色。此外，与疾病抗性相关的miRNA触发了辣椒中phasiRNA的产生，表明对疾病抗性基因家族调控的扩增。其中，miR-n033a-3p（在辣椒中复制了目标NLR）比在马铃薯中定位了更多的属于特定亚组的NLR。随着靶标抗性基因的扩增，靶向抗性基因的miRNA可能已经进化为调控茄科中的许多靶标。这项研究提供了对植物中miRNA及其靶防御基因之间进化关系的见解。其中，miR-n033a-3p（在辣椒中复制了目标NLR）比在马铃薯中定位了更多的属于特定亚组的NLR。随着靶标抗性基因的扩增，靶向抗性基因的miRNA可能已经进化为调控茄科中的许多靶标。这项研究提供了对植物中miRNA及其靶防御基因之间进化关系的见解。其中，miR-n033a-3p（在辣椒中复制了目标NLR）比在马铃薯中定位了更多的属于特定亚组的NLR。随着靶标抗性基因的扩增，靶向抗性基因的miRNA可能已经进化为调控茄科中的许多靶标。这项研究提供了对植物中miRNA及其靶防御基因之间进化关系的见解。