Table_3_The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response.xlsx

The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.

碱性亮氨酸拉链（basic leucine zipper, bZIP）是一类在非生物与生物胁迫响应、植物生长发育过程中发挥关键调控作用的转录因子家族。本研究以鹅掌楸（Liriodendron chinense）为材料，在全基因组范围内开展系统性分析，共鉴定得到45个bZIP转录因子（LchibZIPs），并通过系统发育分析将其划分为13个亚组。同一亚组的蛋白具有相似的基因结构与保守结构域，LchibZIP蛋白中共鉴定出20个保守基序。基因定位分析显示，LchibZIP基因不均匀分布于16条染色体上，且存在4对串联重复基因与9对片段重复基因，据此推测片段重复事件可能与鹅掌楸bZIP基因家族的扩张紧密相关。本研究还分析了鹅掌楸bZIP基因与拟南芥（Arabidopsis thaliana）、水稻（Oryza sativa）的共线性关系，结果表明相较于拟南芥，LchibZIP在进化上与水稻更为接近。顺式作用元件分析显示，归为同一亚家族的LchibZIP基因参与多种生物学功能。此外，本研究通过蛋白-蛋白互作预测与基因本体（Gene Ontology, GO）注释，为后续探索LchibZIP的新功能提出了全新的研究思路。利用转录组测序（RNA-seq）数据与实时荧光定量PCR（qRT-PCR），本研究分析了LchibZIP基因的表达模式，结果显示LchibZIP基因参与低温胁迫调控，其中LchibZIP4与LchibZIP7显著上调表达，LchibZIP2与LchibZIP28则显著下调表达。对鹅掌楸bZIP基因家族的全面鉴定与功能解析，将为鹅掌楸的基因工程与基因功能研究提供重要理论支撑。