Department of Biochemistry and Genetics, Clemson University, Clemson, SC 29631, USA.
BMC Genomics. 2012 Sep 15;13:481. doi: 10.1186/1471-2164-13-481.
MicroRNAs (miRNAs) are small RNAs (sRNAs) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. Within this context, miRNAs and siRNAs are coming to the forefront as molecular mediators of gene regulation in plant responses to annual temperature cycling and cold stress. For this reason, we chose to identify and characterize the conserved and non-conserved miRNA component of peach (Prunus persica (L.) Batsch) focusing our efforts on both the recently released whole genome sequence of peach and sRNA transcriptome sequences from two tissues representing non-dormant leaves and dormant leaf buds. Conserved and non-conserved miRNAs, and their targets were identified. These sRNA resources were used to identify cold-responsive miRNAs whose gene targets co-localize with previously described QTLs for chilling requirement (CR).
Analysis of 21 million peach sRNA reads allowed us to identify 157 and 230 conserved and non-conserved miRNA sequences. Among the non-conserved miRNAs, we identified 205 that seem to be specific to peach. Comparative genome analysis between peach and Arabidopsis showed that conserved miRNA families, with the exception of miR5021, are similar in size. Sixteen of these conserved miRNA families are deeply rooted in land plant phylogeny as they are present in mosses and/or lycophytes. Within the other conserved miRNA families, five families (miR1446, miR473, miR479, miR3629, and miR3627) were reported only in tree species (Populustrichocarpa, Citrus trifolia, and Prunus persica). Expression analysis identified several up-regulated or down-regulated miRNAs in winter buds versus young leaves. A search of the peach proteome allowed the prediction of target genes for most of the conserved miRNAs and a large fraction of non-conserved miRNAs. A fraction of predicted targets in peach have not been previously reported in other species. Several conserved and non-conserved miRNAs and miRNA-regulated genes co-localize with Quantitative Trait Loci (QTLs) for chilling requirement (CR-QTL) and bloom date (BD-QTL).
In this work, we identified a large set of conserved and non-conserved miRNAs and describe their evolutionary footprint in angiosperm lineages. Several of these miRNAs were induced in winter buds and co-localized with QTLs for chilling requirement and bloom date thus making their gene targets potential candidates for mediating plant responses to cold stress. Several peach homologs of genes participating in the regulation of vernalization in Arabidopsis were identified as differentially expressed miRNAs targets, potentially linking these gene activities to cold responses in peach dormant buds. The non-conserved miRNAs may regulate cellular, physiological or developmental processes specific to peach and/or other tree species.
microRNAs (miRNAs) 是大约 21 个核苷酸长的小 RNA (sRNAs)，通过切割或抑制靶基因转录本的翻译来负调控基因表达。在这种情况下，miRNAs 和 siRNAs 作为植物对年度温度循环和冷胁迫反应的基因调控的分子介质崭露头角。出于这个原因，我们选择鉴定和表征桃（Prunus persica (L.) Batsch）的保守和非保守 miRNA 成分，重点关注桃的全基因组序列和代表非休眠叶和休眠芽的两种组织的 sRNA 转录组序列。鉴定了保守和非保守 miRNA 及其靶标。这些 sRNA 资源用于鉴定冷响应 miRNA，其基因靶标与先前描述的冷需求 (CR) 相关的 QTL 共定位。
对 2100 万桃 sRNA 读数的分析使我们能够鉴定出 157 个和 230 个保守和非保守 miRNA 序列。在非保守 miRNA 中，我们鉴定出 205 个似乎是桃特有的。桃与拟南芥的比较基因组分析表明，除了 miR5021 之外，保守 miRNA 家族在大小上相似。这 16 个保守 miRNA 家族在陆地植物系统发育中根深蒂固，因为它们存在于苔藓植物和/或石松植物中。在其他保守 miRNA 家族中，有五个家族（miR1446、miR473、miR479、miR3629 和 miR3627）仅在树种（杨桃、三叶杨和桃）中报道。表达分析鉴定了冬季芽与幼叶相比表达上调或下调的几个 miRNA。对桃蛋白组的搜索允许预测大多数保守 miRNA 和大量非保守 miRNA 的靶基因。桃的预测靶标中有一部分在其他物种中尚未报道。几个保守和非保守 miRNA 和 miRNA 调节基因与冷需求 (CR-QTL) 和开花日期 (BD-QTL) 的数量性状基因座 (QTL) 共定位。
在这项工作中，我们鉴定了一大组保守和非保守 miRNA，并描述了它们在被子植物谱系中的进化足迹。这些 miRNA 中的一些在冬季芽中诱导表达，并与冷需求和开花日期的 QTL 共定位，从而使它们的基因靶标成为介导植物对冷胁迫反应的潜在候选基因。在拟南芥中参与春化调控的几个桃同源基因被鉴定为差异表达 miRNA 的靶标，这可能将这些基因活性与桃休眠芽中的冷反应联系起来。非保守 miRNA 可能调节桃和/或其他树种特有的细胞、生理或发育过程。
