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糜子(Panicum miliaceum L.)全基因组YABBY基因家族鉴定与高渗溶液胁迫下表达特征

Genome-wide Identification and Expression Characteristics of the YABBY Gene Family under Hypertonic Solution Stress in Broomcorn Millet (Panicum miliaceum L.)

  • 摘要: 为系统了解糜子(Panicum miliaceum L.)YABBY基因家族成员及其特征,基于糜子基因组和注释数据,使用生物信息学的方法,鉴定分析了YABBY转录因子家族成员、染色体分布、蛋白特征、基因结构、进化关系、保守结构域、启动子区域的顺式作用元件及高渗溶液胁迫下表达特征。结果表明:糜子中含有17个YABBY基因,分别位于第1、2、3、4、5、6、12、15、16号染色体上,PmYABBY蛋白长度为125~935个氨基酸,等电点为5.70~10.33,家族成员含有3~13个内含子,通过亚细胞定位预测,所有成员都定位在细胞核中。利用MEGA7.0软件对拟南芥(Arabidopsis thaliana)、水稻(Oryza sativa)、玉米(Zea mays)、谷子(Setaria italica)和糜子YABBY基因家族的系统进化分析表明,17个糜子YABBY基因分为YAB1/YAB3、YAB2、CRC和INO 4个亚族。采用PlantCARE软件分析顺式作用元件发现,在糜子YABBY基因上游2 000 bp序列中,存在大量光应答和激素响应等种类和数目不同的顺式作用元件,表明该家族基因表达与光、激素等因素密切相关。幼苗期不同时间点PEG-6000高渗溶液胁迫下转录组测序数据分析显示,PmYABBY5、PmYABBY8、PmYABBY12、PmYABBY7、PmYABBY13、PmYABBY2、PmYABB9和PmYABBY7分别在地上器官(茎叶)、地下器官(根)中表达量变化较大,说明YABBY基因家族成员参与了非生物胁迫响应。研究结果可为糜子PmYABBY基因进一步功能解析和遗传利用提供科学依据。

     

    Abstract: To systematically understand the members and characteristics of the YABBY gene family in broomcorn millet(Panicum miliaceum L.), based on its genome and annotation data, bioinformatics method were adopted to analyze and identify members of gene family, chromosomal distribution, protein characteristics, gene structure, evolutionary relationships, conserved domains, cis-elements of promoter region and expression characteristics under hypertonic solution stress. There are 17 YABBY genes in broomcorn millet, which are distributed on chromosomes 1, 2, 3, 4, 5, 6, 12, 15 and 16. The length of PmYABBY protein ranges from 125 to 935 amino acids and the isoelectric point is between 5.70 and 10.33. The family members contain 3 to 13 introns. By cell localization prediction, all the members were located in the nucleus. MEGA7.0 software was adopted to perform the phylogenetic analysis of YABBY gene families in Arabidopsis thaliana, Oryza sativa, Zea mays, Setaria italica and Panicum miliaceum, showing that the 17 YABBY genes were divided into four subfamilies in broomcorn millet, namely, YAB1/YAB3, YAB2, CRC and INO. Using PlantCare software to analyze the cis-acting elements in the 2 000 bp sequence of YABBY gene in broomcorn millet found that there were a large number of cis-acting elements with different types and numbers, such as light response and hormone response, in the 2 000 bp sequence upstream of the YABBY gene, indicating that the gene expression of this family was closely related to light and hormone factors. Analysis of transcriptome sequencing data under PEG-6000 hypertonic solution stress at different time points in seedling stage showed that PmYABBY5, PmYABBY8, PmYABBY12, PmYABBY7, PmYABBY13, PmYABBY2, PmYABBY9 and PmYABBY7 had obvious change in aboveground organs(stems and leaves) and underground organs(roots), respectively, indicating that members of YABBY gene family were involved in abiotic stress response. These results provided scientific basis for further functional dissection and genetic utilization of PmYABBY genes in broomcorn millet.

     

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