基于转录组的楠木MYB转录因子的挖掘及分析

Transcriptome-based excavation and analysis of MYB family transcription factors in Phoebe zhennan

关键词:  楠木, 转录组, MYB转录因子, 生物信息学, 基因表达

Key words:  Phoebe zhennan, transcriptome, MYB transcription factors, bioinformatics, gene expression

摘要:

楠木(Phoebe zhennan)为樟科常绿乔木,是国家二级重点保护树种。楠木生长缓慢,木材形成所需周期较长,其原因有待进一步深入分析。近年来转录因子已成为植物分子生物学研究的热点,高通量测序技术的应用和发展促进了转录因子的挖掘和深入分析。该研究基于我国特有濒危树种楠木的转录组数据,通过与拟南芥基因组MYB转录因子进行对比,对楠木MYB转录因子进行挖掘和生物信息学分析,并结合功能预测和不同组织表达对其进行深入分析。结果表明:从楠木转录组数据中,共挖掘出82个MYB转录因子,这82个MYB转录因子蛋白质所含氨基酸数目为50～1 121个、分子量为5.907～123.64 kDa,整体表现为亲水性不稳定蛋白,以α-螺旋和无规则卷曲为主要二级结构元件。序列比对和进化树分析表明,楠木MYB转录因子的结构域有高度保守性,含有[W]-X(19)-[W]-X(19)结构; 82个PzMYB可分为22类,参与生长发育、次生代谢、逆境响应等过程,与功能预测分析结果相一致。同时,在楠木茎和叶中,差异表达PzMYB数目为18个,其中上调10个、下调8个。该研究结果不仅对楠木MYB转录因子的挖掘和功能分析以及分子生物学研究奠定了基础,而且还对其遗传改良和分子育种具有参考价值。

Abstract:

Phoebe zhennan is an endemic valuable tree to China and listed as one of the national second-class protected wild plants. The growth rate of P. zhennan is too slow and the operating cycle is too long. To date, there is no reason to explain this phenomenon. These years have witnessed transcription factors becoming a focus on the researches about plants molecular biology, as the high-throughput sequencing technology has been well applied and developed. In the present study, the identification and phylogenetic analysis of the P. zhennan MYB(PzMYB)transcription factor family was performed and the expression profiles of these genes were determined. PzMYBs were identified from the P. zhennan transcriptome using bioinformatics tools, and their putative functions were determined based on the phylogenetic tree and classified into subfamilies using AtMYBs describing known functions. The results showed that 82 PzMYB transcription factors were excavated, and they encoded 50-1 121 amino acids, predicting hydrophilic and unstable. Their main structural elements were α-helix and irregular curl. Also, the sequence analysis and construction of phylogenetic tree showed that these MYB transcription factors had a certain conserved type, containing [W]-X(19)-[W]-X(19). Eighty-two PzMYB could be divided into 22 categories, and were related to the plant response to biotic stresses, cell development, secondary metabolism etc. Their involvements in response to stresses were reported by several transcriptional studies, which was precisely consistent with the functional prediction. Lastly, the members in the same subfamily had different spatial and temporal expression profiles, with genes in stems and leaves expressed at various levels, which was precisely consistent with the functional prediction. In stem, the numbers of differential expression of genes were eighteen, ten up-regulated and eight down-regulated in leaf. Based on the transcriptome data of P. zhennan, an endemic tree in China, we excavated and analyzed its MYB transcription factors, and provided valuable information for PzMYB gene cloning and functional characterization of P. zhennan. This research will lay a foundation for the study of molecular biology of P. zhennan and provide references for its genetic modification and molecular breeding.