Abstract U-box is the protein domain, which was presented in proteins of yeasts to higher organisms. The U-box domain-contains proteins encoded by the U-box gene family, which is a huge gene family in plants. However, information about all U-box genes in apple, one of the most popular fruits all around the world is not clear and organized. In the present study, identification of the apple U-box genes was performed based on its whole-genome sequence. From the analysis, 69 U-box genes were found in apple according to the U-box domain. The U-box genes of apple distributed across all the 17 chromosomes at different densities. Phylogenetic analysis of U-box genes between apple and Arabidopsis thaliana suggested that the genes can be clustered into seven subgroups (I–VII) on the basis of their structural and phylogenetic features. Sixty-nine U-box genes and the structure of the encoded proteins were identified in apple. The RNA-seq results showed that 23 (56.1% of the detectable genes) U-box genes were found up-regulated and 18 (43.9% of the detectable genes) U-box genes were found down-regulated under P. expansum infection stress. RT-qPCR results showed the same trend with the transcriptome. The RT-qPCR validation showed that the results obtained in the transcriptomic analysis were accurate. The U-box genes of apple were strongly expressed during P. expansum infection. These results suggested that the U-box gene family of apple may play important role in the resistance mechanism of apple against P. expansum infection. This systematic research provided a foundation for further functional investigation of U-box genes with the aim of improving apple production.

中文翻译：

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苹果U-box泛素-蛋白质连接酶基因家族全基因组调查与分析：扩展青霉感染过程中的表达谱

摘要 U-box是一个蛋白质结构域，它存在于酵母的蛋白质中，呈现给高等生物。U-box结构域-包含由U-box基因家族编码的蛋白质，这是植物中一个庞大的基因家族。然而，关于苹果这个世界上最受欢迎的水果之一的所有 U-box 基因的信息并不清晰和有条理。在本研究中，苹果 U-box 基因的鉴定是基于其全基因组序列进行的。经分析，根据U-box结构域，在苹果中发现了69个U-box基因。苹果的U-box基因以不同的密度分布在全部17条染色体上。苹果和拟南芥之间 U-box 基因的系统发育分析表明，根据其结构和系统发育特征，这些基因可以分为七个亚组（I-VII）。在苹果中鉴定了 69 个 U-box 基因和编码蛋白的结构。RNA-seq结果显示，在P. expansum感染胁迫下，发现23个（可检测基因的56.1%）U-box基因上调，18个（可检测基因的43.9%）U-box基因下调. RT-qPCR 结果显示出与转录组相同的趋势。RT-qPCR 验证表明转录组学分析中获得的结果是准确的。苹果的 U-box 基因在 P. expansum 感染期间强烈表达。这些结果表明，苹果的U-box基因家族可能在苹果抗扩展P. expansum感染的抗性机制中起重要作用。该系统研究为进一步研究U-box基因以提高苹果产量提供了基础。