MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets; 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets; 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome.

中文翻译：

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胡桃和小叶锦鸡儿基因组中保守的miRNA及其假定靶基因的计算鉴定和比较分析

微小RNA（miRNA）是动植物蛋白质编码基因转录后调控的重要因素。通过对小RNA测序或通过计算发现它们。我们采用了基于序列同源性的计算方法，以在波斯（英语）胡桃，核桃和其北美野生近缘种J. microcarpa中鉴定保守的miRNA及其靶基因。在regia J.基因组中共检测到119个miRNA前体（pre-miRNA），在J. microcarpa基因组中检测到121个，预测了miRNA目标基因，并在两个基因组中进行了功能注释。在J. regia基因组中，有325种不同的基因是靶标；转录切割调节了87.08％，翻译抑制调节了12.92％。在J. microcarpa基因组中，有316种不同的基因是目标。88.92％受转录切割调控，11.08％受翻译抑制调控。migias分别在regia和J. microcarpa基因组中分别对所有抗性基因类似物（RGA）的1.3％和2.0％以及所有转录因子（TFs）的2.7％和2.6％进行调控。胡桃基因组是由全基因组复制（WGD）进化而来的，由八对分离的同源染色体组成。在每对染色体中，具有更多平均转录水平更高的基因的染色体也比其同源同源物具有更多的前miRNA和更多的靶基因。尽管在瑞格斯氏菌和微果蝇J.基因组之间的pre-miRNA中仅检测到很小的差异，但每个基因组内同源染色体之间的pre-miRNA基因座中约没有三分之一是保守的。Pre-miRNA及其相应的靶基因显示出在亚基因组内并置的趋势。