葡萄WD40基因家族鉴定及表达量分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-0274

摘要/Abstract

摘要：

目的 WD40超家族广泛存在于真核生物中，具有作为蛋白质复合物支架的基本亚基。WD40蛋白在植物发育和生理过程中发挥重要的调控作用。解析葡萄VvWD40基因家族成员的序列结构和理化性质，了解其在葡萄果实发育过程中的作用，为葡萄分子育种提供基因资源。方法基于葡萄全基因组信息，利用生物信息学方法对VvWD40家族进行鉴定，并对家族成员理化性质、染色体分布、基因结构、蛋白保守结构、系统进化、启动子顺式作用元件以及组织表达特性等进行分析，进一步利用转录组及RT-qPCR分析VvWD40基因在‘早黑宝’葡萄不同发育时期的表达模式。结果在葡萄基因组鉴定出86个WD40基因，通过系统发育分析将其分为7个组。在葡萄中共鉴定出12对共线基因对。Ka/Ks分析表明，它们在进化过程中主要经历了纯化选择。顺式作用元件分析表明，VvWD40基因家族含有激素及胁迫响应顺式作用元件，这些元件与葡萄果实发育密切相关。其中，VvWD40-62/84含有类黄酮合成元件，表明它们可能与花青素合成有关。‘早黑宝’葡萄4个不同阶段的表达谱分析显示，大多数VvWD40s在果实发育过程中表达。通过RT-qPCR验证8个基因在‘早黑宝’葡萄发育过程中表达量变化情况，VvWD40-34/49基因在葡萄果实发育初期表达量较低，成熟时期表达量最高，表明这2个基因可能在葡萄果实发育转色过程中发挥关键作用。结论葡萄中鉴定出86个VvWD40基因，不均匀地分布在19条染色体上。大部分VvWD40在葡萄果实发育过程中表达量变化显著，表明其在葡萄生长发育中发挥重要作用。

关键词: 葡萄, WD40基因, 基因家族, 生信分析, 果实发育, 表达分析

Abstract:

Objective The WD40 superfamily is widely present in eukaryotes and serves as a basic subunit of protein complexes. WD40 proteins play important regulatory roles in plant development and physiology. This study aims to analyze the sequence structure and physicochemical properties of VvWD40 gene family members in grapes, understand the role of grape WD40 genes in fruit development, and provide genetic resources for grape molecular breeding. Method Based on the grape genome information, bioinformatics methods were used to identify the VvWD40 family, and to analyze the physicochemical properties, chromosomal distribution, gene structure, conserved protein structures, phylogenetic evolution, cis-acting elements in the promoter, and tissue expression characteristics of the family members. Further, transcriptome and RT-qPCR were combined to analyze the expression patterns of VvWD40 genes in different developmental stages of ‘Zaoheibao’ grapes. Result A total of 86 WD40 genes were identified in the grape genome and classified into 7 groups through phylogenetic analysis. A total of 12 pairs of collinear gene pairs were identified in the grape. Ka/Ks analysis indicated that they mainly experienced purifying selection during evolution. The cis-acting element analysis showed that the VvWD40 gene family contained hormone and stress response cis-acting elements, which were closely related to grape fruit development. Among them, VvWD40-62/84 contained flavonoid-synthezing elements, suggesting that they might be related to anthocyanin synthesis. The expression profiles of 4 different stages of ‘Zaoheibao’ grape were analyzed, and it was found that most VvWD40 were expressed during fruit development. The expressions of 8 genes during the development of ‘Zaoheibao’ grape were verified by RT-qPCR. The expressions of VvWD40-34/49 genes were relatively low at the early stage of grape fruit development and the highest at the mature stage, indicating that these two genes might play a key role in the color change process of grape fruit development. Conclusion The 86 VvWD40 genes are identified, which are unevenly distributed on 19 chromosomes. Most VvWD40 show significant expression variations during grape fruit development, suggesting their important roles in grape growth and development.

Key words: Vitis vinifera L., WD40 gene, gene family, bioinformatics analysis, fruit development, expression analysis

张高翔, 吴玉碧, 郭亚静, 纪薇, 杨忠义. 葡萄WD40基因家族鉴定及表达量分析[J]. 生物技术通报, doi: 10.13560/j.cnki.biotech.bull.1985.2025-0274.

ZHANG Gao-xiang, WU Yu-bi, GUO Ya-jing, JI Wei, YANG Zhong-yi. Identification and Expression Analysis of WD40 Gene Family in Grape[J]. Biotechnology Bulletin, doi: 10.13560/j.cnki.biotech.bull.1985.2025-0274.

图/表 12

表1 引物信息

Table 1 Primer information

基因 Gene	正向引物 Forward primer （5′‒3′）	反向引物 Reverse primer （5′‒3′）
WD40-3	F： TTGGAAGGACACGAGAAACC	R： GGATACCTGCCACACCTTAATC
WD40-9	F： GACTTCCTCAAGAGCTCCATAAA	R： GTCCAAGCTCAAGCAAGAAAC
WD40-27	F： GTTCCTTCGATGAGACCGTTAG	R： GAGCCATCACGATTGAAATTGG
WD40-34	F： CAGTTTAGAGAGCGGCAAGAA	R： GTCCGTACAGCCATGTCATTAG
WD40-42	F： AGTGCCAGCAAGGATTCTAC	R： TCTAGGCTGCAACTCCAAAC
WD40-49	F： GTGAGGACTCAAAGGTGTATGT	R： GGACTCCAGCTCACACAATTA
WD40-51	F： CGTGCGATCTCTCGTGTATT	R： GCTCTTTCCCTCAGCATCATA
WD40-77	F： CTGACTCGCCACAGGAATATC	R： CTTTCACCGACCAGACATAGAG
EF1α	F： GAACTGGGTGCTTGATAGGC	R： ACCAAAATATCCGGAGTAAAAGA

图1 VvWD40基因家族进化树

Fig. 1 Evolutionary treeof VvWD40 gene family

图2 VvWD40基因家族染色体位置

Fig. 2 Chromosome position of VvWD40 gene family

图3 VvWD40基因家族motif（A）、结构域（B）、基因结构（C）分析

Fig. 3 Analysis of the motif (A), domain (B) , and gene structure (C) of the VvWD40 gene family

图4 VvWD40基因家族启动子顺式作用元件分析

Fig. 4 Cis-acting elements analysis in VvWD40 gene family promoter

图5 VvWD40基因家族顺式作用元件交集分析

Fig. 5 Intersection analysis of cis-acting elements of VvWD40 gene family

图6 VvWD40基因家族密码子相关性分析

Fig. 6 Correlation analysis of codons in the VvWD40 gene family

图7 VvWD40基因在葡萄不同组织及不同时期的表达量分析

Fig. 7 Analysis of VvWD40 gene expressions in different tissues and different periods of grape

图8 VvWD40基因家族共线性分析

Fig. 8 Collinearity analysis of VvWD40 gene family

图9 VvWD40基因家族选择压力分析

Fig. 9 Analysis of selective pressure on the VvWD40 gene family

图10 VvWD40基因家族蛋白互作网络分析（A）、GO功能注释（B）和KEGG富集分析（C）

Fig. 10 Protein interaction network analysis of the VvWD40 gene family (A), GO functional annotation (B), and KEGG enrichment analysis

图11 VvWD40基因家族表达模式分析及RT-qPCR验证EL33：浆果仍然坚硬且呈绿色；EL35：浆果开始着色并增大；EL36：浆果具有中等可溶性固形物含量；EL38：浆果收获成熟。不同小写字母表示存在显著差异（P<0.05）

Fig. 11 Analysis of the expression pattern of the VvWD40 gene family and RT-qPCR verificationEL33: The berries are still firm and green. EL35: The berries start to color and increase in size. EL36: The berries have a medium content of soluble solids. EL38: The berries are ready for harvest and fully mature. Different lowercase letters indicate significant differences (P<0.05)

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