Wang Guo-Ming, Yin Hao, Qiao Xin, Tan Xu, Gu Chao, Wang Bao-Hua, Cheng Rui, Wang Ying-Zhen, Zhang Shao-Ling
Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
Plant Sci. 2016 Dec;253:164-175. doi: 10.1016/j.plantsci.2016.09.009. Epub 2016 Sep 29.
F-box gene family, as one of the largest gene families in plants, plays crucial roles in regulating plant development, reproduction, cellular protein degradation and responses to biotic and abiotic stresses. However, comprehensive analysis of the F-box gene family in pear (Pyrus bretschneideri Rehd.) and other Rosaceae species has not been reported yet. Herein, we identified a total of 226 full-length F-box genes in pear for the first time. And these genes were further divided into various subgroups based on specific domains and phylogenetic analysis. Intriguingly, we observed that whole-genome duplication and dispersed duplication have a major contribution to F-box family expansion. Furthermore, the dynamic evolution for different modes of gene duplication was dissected. Interestingly, we found that dispersed and tandem duplicate have been evolving at a high rate. In addition, we found that F-box genes exhibited functional specificity based on GO analysis, and most of the F-box genes were significantly enriched in the protein binding (GO: 0005515) term, supporting that F-box genes might play a critical role for gene regulation in pear. Transcriptome and digital expression profiles revealed that F-box genes are involved in the development of multiple pear tissues. Overall, these results will set stage for elaborating the biological role of F-box genes in pear and other plants.
F-box基因家族作为植物中最大的基因家族之一，在调控植物发育、繁殖、细胞蛋白质降解以及对生物和非生物胁迫的响应中发挥着关键作用。然而，尚未见关于梨（Pyrus bretschneideri Rehd.）及其他蔷薇科物种中F-box基因家族的全面分析报道。在此，我们首次在梨中总共鉴定出226个全长F-box基因。并且基于特定结构域和系统发育分析，将这些基因进一步划分为不同的亚组。有趣的是，我们观察到全基因组重复和分散重复对F-box家族的扩张有主要贡献。此外，剖析了基因重复不同模式的动态进化。有意思的是，我们发现分散重复和串联重复一直在高速进化。另外，基于基因本体（GO）分析，我们发现F-box基因表现出功能特异性，并且大多数F-box基因在蛋白质结合（GO: 0005515）条目上显著富集，这支持了F-box基因可能在梨的基因调控中起关键作用。转录组和数字表达谱显示F-box基因参与多个梨组织的发育。总体而言，这些结果将为阐明F-box基因在梨及其他植物中的生物学作用奠定基础。
