Esposito Salvatore, Aversano Riccardo, Tripodi Pasquale, Carputo Domenico
CREA Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy.
Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
Plants (Basel). 2021 May 18;10(5):1004. doi: 10.3390/plants10051004.
Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs' precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species ( L., L., L. Fort., and Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.
全基因组加倍（多倍体化）在被子植物中很常见。多项研究表明，它通常与分子、生理和表型变化有关。越来越多的证据指出，微小RNA（miRNA）可能在全基因组加倍中发挥重要作用。然而，仍缺乏一种比较多倍体中miRNA表达的综合方法。在此，我们对已发表的RNAseq数据集进行了重新分析，以鉴定五个物种（[物种名称1]、[物种名称2]、[物种名称3]、[物种名称4]和[物种名称5]）二倍体（2x）和四倍体（4x）中的微小RNA前体（pre-miRNA）。我们发现了3568个pre-miRNA，其中三个（pre-miR414、pre-miR5538和pre-miR5141）在所有二倍体中都很丰富，而在它们的四倍体对应物中不存在/含量很低。预计它们靶向不止一个mRNA转录本，许多转录本属于转录因子（TF）、DNA修复机制且与胁迫相关。在所有二倍体和四倍体中共同发现了16个pre-miRNA。其中，pre-miRNA482、pre-miRNA2916和pre-miRNA167在多倍体化后改变了表达，在四倍体植物中被诱导或抑制。基于我们的结果，在所有被研究的物种中都触发了一种常见的倍性依赖性反应，这涉及DNA修复、ATP合成、萜类生物合成以及一些胁迫响应转录本。此外，仅对[物种名称6]的二倍体与四倍体样本进行的特定pre-miRNA表达分析表明，倍性依赖性pre-miRNA似乎积极调节核苷酸代谢，可能是为了应对因DNA含量增加而对DNA构建块的需求增加。总体而言，这些结果概述了植物中同源多倍体化后miRNA介导反应的关键作用。
