摘要
【目的】通过生物信息学分析明确LBD转录因子在葡萄基因组中的数量、结构和非生物胁迫差异表达,为探究LBD转录因子在葡萄非生物胁迫中的作用奠定理论基础。【方法】根据已经报道的拟南芥LBD基因,利用葡萄基因组数据库中的BLAST软件鉴定葡萄基因组中的LBD基因。采用DNAMAN5.0、Clustalx、MapInspect、MEME、GSDS2.0、ExPASy和MEGA5.0等软件进行生物信息学分析。利用PLEXdb中葡萄Affymetrix GeneChip 16K基因芯片数据绘制芯片表达谱。采用qRT-PCR方法检测VvLBD基因家族在逆境胁迫中的表达情况。【结果】从葡萄(Vitis vinifera L.)全基因组中鉴定得到30个LBD基因家族成员,可分为ClassⅠ和ClassⅡ两类,ClassⅠ分为5个亚族,分别是Ⅰa、Ⅰb、Ⅰc、Ⅰd和Ⅰe,ClassⅡ分为2个亚族,分别是Ⅱa和Ⅱb。理化性质分析表明,VvLBD基因家族编码氨基酸数目介于127—386,理论等电点分布在4.77—9.28。定位分析发现,该基因家族的30个基因分布于葡萄19条染色体中的11条染色体上,其中第13染色体上分布最多,有7个基因。多序列比对和motif分析结果表明,VvLBD基因家族具有特定的3个保守结构域,分别是类锌指结构、亮氨酸拉链结构和甘氨酸-丙氨酸-丝氨酸(GAS)结构。亚细胞定位分析表明,VvLBD基因家族主要在叶绿体、线粒体和细胞核中进行表达。VvLBD基因家族的二级结构主要以α-螺旋和不规则卷曲为主。VvLBD基因芯片表达谱分析发现,大部分基因在盐胁迫和PEG胁迫下表达量上升,并且胁迫时间的长短对该基因家族成员的表达也存在差异。qRT-PCR分析结果表明,VvLBD基因家族成员中VvLBD8、VvLBD11、VvLBD12、VvLBD15、VvLBD16、VvLBD17在400 mmol·L-1 NaCl处理条件下呈上调表达,表达量分别是对照的3、1、8、4、5和13倍,VvLBD12和VvLBD19在10%PEG处理条件下呈上调表达,表达量分别是对照的4和26倍。【结论】从葡萄基因组中一共鉴定出30个
【Objective】The objectives of this research are to identify the Lateral Organ Boundaries Domain（LBD） family genes from grape（Vitis vinifera） genome, to know the profile of LBD family such as gene number, gene structure and abiotic stress expression characteristics in grape, and to provide theoretical basis for exploring what roles the LBD transcription factors play in abiotic stress of grape.【Method】The LBD genes in grape genome-wide were identified by BLAST software in the grape genome database based on LBD genes have been reported from Arabidopsis. DNAMAN5.0, Clustalx, Map Inspect, MEME, GSDS2.0, Ex PASy and MEGA5.0 software were used for carry out various bioinformatics analysis of LBD. The expression profile chip was draw by the data comes from Affymetrix Gene Chip 16 K in PLEXdb. The qRT-PCR was used to detect the expression of grape LBD gene family in abiotic stress.【Result】Total of 30 LBD genes were identified from grape genome, which can be divided into ClassⅠand ClassⅡ. The classⅠcan be divided into 5 subtribe which are namedⅠa,Ⅰb,Ⅰc,Ⅰd andⅠe. ClassⅡ can be divided into Ⅱa and Ⅱb. The number of amino acids is between 127 and 386, and the theoretical equivalence point is between 4.77 and 9.28 in the VvLBD gene family by physicochemical analysis. The analysis of the gene＇s location on the chromosome revealed that the 30 genes in this family were distributed on 11 of the 19 chromosomes of the grape, and the chromosome 13 contains 7 genes. Multiple sequence alignments and Motif analysis showed that the VvLBD gene family has three conserved domains, namely the sinusoidal structure, the leucine zipper structure, and the Glycine-alanine-serine（GAS） structure. The VvLBD gene family is mainly expressed in chloroplast, mitochondria and nucleus through the sub-cellular location analyzing. The alpha-helix and irregular curl are the main structure of the secondary structure in the VvLBD gene family. The expression of the most gene was increased under the salt and PEG str
作者
何红红
马宗桓
张元霞
张娟
卢世雄
张志强
赵鑫
吴玉霞
毛娟
HE HongHong;MA ZongHuan;ZHANG YuanXia;ZHANG Juan;LU ShiXiong;ZHANG ZhiQiang;ZHAO Xin;WU YuXia;MAO Juan(College of Horticulture,Gansu Agricultural University,Lanzhou,73007)
出处
《中国农业科学》
CAS
CSCD
北大核心
2018年第21期4102-4118,共17页
Scientia Agricultura Sinica
基金
甘肃农业大学大学生科研训练项目
国家自然科学基金(31460500)
