苹果NF-YA转录因子家族的生物信息学和表达分析

王寻1,冯资权1,由春香1,韩月彭2,王小非1,郝玉金1,*
1山东农业大学园艺科学与工程学院, 作物生物学国家重点实验室, 山东果蔬优质高效生产协同创新中心, 山东 泰安271018;2中国科学院武汉植物园, 中国科学院植物种质创新与特色农业重点实验室, 武汉430074

通信作者:郝玉金;E-mail: haoyujin@sdau.edu.cn

摘 要:

NF-YA是植物中一类保守的转录因子, 广泛参与调控植物生长发育与响应胁迫。苹果(Malus pumila) GDDH13高质量参考基因组的释放, 为本文NF-YA的全基因组分析提供了基础。基于蛋白同源比对与结构域模型扫描2种生物信息学方法, 共筛选出11个苹果NF-YA (MpNF-YA)成员, 它们均包含CBFB_NF-YA核心保守结构域, 亚细胞定位预测都位于细胞核中。 MpNF-YA分布于10条染色体上, 具有相似的基因组结构与内含子相位组成。结构域序列比较发现, 它们的保守域由2个典型区段(A1A2)构成。遗传进化与保守基序分析表明, 11MpNF-YA分为3, 且都具有motif 1motif 2。顺式元件扫描、 miRNA预测及表达模式分析暗示MpNF-YA基因受多种调控因素影响, 呈现组织差异表达的特点, 并且在果实发育与氮饥饿响应等环节起到重要作用。

关键词:苹果; NF-YA; 生物信息学; 核心保守结构域; 遗传进化; 表达模式

收稿:2020-09-29   修定:2020-11-15

资助:国家重点研发计划项目(2018YFD1000100)、国家现代苹果产业技术体系项目(CARS-27)、山东省农业良种工程项目(2019LZGC007) 和云南省科技计划项目(2019ZG002-1-03)

Bioinformatics and expression analysis of NF-YA transcription factor family in apple

WANG Xun1, FENG Ziquan1, YOU Chunxiang1, HAN Yuepeng2, WANG Xiaofei1, HAO Yujin1,*
1Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efciency, State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China; 2Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China

Corresponding author: HAO Yujin; E-mail: haoyujin@sdau.edu.cn

Abstract:

NF-YA is a conservative transcription factor in plants, widely involved in regulating plant growth
and development and responding stress. The release of high-quality apple reference genome GDDH13 provides the basis for the genome-wide analysis of
NF-YA in this paper. Based on the two bioinformatics
methods, protein homology alignment and domain model scanning, a total of 11 apple NF-YA (MpNF-YA) members were screened out. All of them contain CBFB_NF-YA core conservative domain, and are located in the nucleus through subcellular localization prediction.
MpNF-YAs are distributed on 10 chromosomes and have similar genomic structure and intron phase composition. Comparison of domain sequences shows that their conserved domains consist of two typical domains (A1 and A2). Genetic evolution and conserved motifs analyses show that the 11 MpNF-YAs are divided into 3 groups, and all the members have motif 1 and motif 2. Cis-element scanning, miRNA prediction and expression pattern analyses suggest that MpNF-YA genes are affected by various regulatory factors, present the characteristics of differential expression in tissues, and play an important role in fruit development and nitrogen starvation response.

Key words: apple; NF-YA; bioinformatics; core conservative domain; genetic evolution; expression pattern

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