Zhu Youyin, Li Yongqiang, Xin Dedong, Chen Wenrong, Shao Xu, Wang Yue, Guo Weidong
College of Agricultural and Biological Engineering, Jinhua Polytechnic, Jinhua, Zhejiang 321007, China; Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China.
Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China.
Gene. 2015 Jan 25;555(2):362-76. doi: 10.1016/j.gene.2014.11.032. Epub 2014 Nov 15.
Bud dormancy is a critical biological process allowing Chinese cherry (Prunus pseudocerasus) to survive in winter. Due to the lake of genomic information, molecular mechanisms triggering endodormancy release in flower buds have remained unclear. Hence, we used Illumina RNA-Seq technology to carry out de novo transcriptome assembly and digital gene expression profiling of flower buds. Approximately 47million clean reads were assembled into 50,604 sequences with an average length of 837bp. A total of 37,650 unigene sequences were successfully annotated. 128 pathways were annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and metabolic, biosynthesis of second metabolite and plant hormone signal transduction accounted for higher percentage in flower bud. In critical period of endodormancy release, 1644, significantly differentially expressed genes (DEGs) were identified from expression profile. DEGs related to oxidoreductase activity were especially abundant in Gene Ontology (GO) molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that DEGs were involved in various metabolic processes, including phytohormone metabolism. Quantitative real-time PCR (qRT-PCR) analysis indicated that levels of DEGs for abscisic acid and gibberellin biosynthesis decreased while the abundance of DEGs encoding their degradation enzymes increased and GID1 was down-regulated. Concomitant with endodormancy release, MADS-box transcription factors including P. pseudocerasus dormancy-associated MADS-box (PpcDAM), Agamous-like2, and APETALA3-like genes, shown remarkably epigenetic roles. The newly generated transcriptome and gene expression profiling data provide valuable genetic information for revealing transcriptomic variation during bud dormancy in Chinese cherry. The uncovered data should be useful for future studies of bud dormancy in Prunus fruit trees lacking genomic information.
芽休眠是中国樱桃（Prunus pseudocerasus）在冬季存活的关键生物学过程。由于缺乏基因组信息，触发花芽内休眠解除的分子机制尚不清楚。因此，我们利用Illumina RNA-Seq技术对花芽进行了从头转录组组装和数字基因表达谱分析。大约4700万个clean reads被组装成50604个序列，平均长度为837bp。共成功注释了37650个单基因序列。通过京都基因与基因组百科全书（KEGG）通路分析注释了128条通路，其中代谢、次生代谢物生物合成和植物激素信号转导在花芽中占比更高。在内休眠解除的关键时期，从表达谱中鉴定出1644个显著差异表达基因（DEGs）。与氧化还原酶活性相关的DEGs在基因本体（GO）分子功能类别中尤为丰富。KEGG通路分析表明，DEGs参与了包括植物激素代谢在内的各种代谢过程。定量实时PCR（qRT-PCR）分析表明，脱落酸和赤霉素生物合成的DEGs水平下降，而编码其降解酶的DEGs丰度增加，且GID1下调。伴随着内休眠的解除，包括中国樱桃休眠相关MADS-box（PpcDAM）、类AGAMOUS2和类APETALA3基因在内的MADS-box转录因子发挥了显著的表观遗传作用。新生成的转录组和基因表达谱数据为揭示中国樱桃芽休眠期间的转录组变异提供了有价值的遗传信息。这些发现的数据应有助于未来对缺乏基因组信息的李属果树芽休眠的研究。
