番茄VPE基因家族鉴定和抗逆功能分析

doi:10.13560/j.cnki.biotech.bull.1985.2026-0160

摘要/Abstract

摘要：

目的系统鉴定番茄液泡加工酶（vacuolar processing enzyme, VPE）基因家族成员，解析其进化关系、表达模式及在非生物胁迫响应中的潜在功能。方法利用生物信息学方法鉴定SlVPE家族成员，并对其理化性质、系统进化、基因结构、保守域、染色体分布、顺式作用元件及种间共线性进行系统分析；整合公共转录组数据与RT-qPCR技术，分析该家族的组织特异性表达模式及其在干旱、高低温、盐、碱及盐碱混合胁迫下的表达响应。结果在番茄中鉴定到13个含有Peptidase_C13与legumain_C结构域的SlVPE基因，分为3个亚家族。除SlVPE4和SlVPE5外，所有成员以基因簇的形式聚集于第8染色体。表达分析表明，SlVPE家族具有明显组织及时空特异性，SlVPE3、SlVPE5为组成型高表达基因，SlVPE2、SlVPE7为果实特异性高表达基因；非生物胁迫下，家族整体响应以表达抑制为主，SlVPE3为干旱、盐及盐碱混合胁迫的核心响应基因，SlVPE7受碱胁迫特异性诱导，SlVPE8主要响应高温和低温胁迫。根据野生种醋栗番茄和栽培番茄的序列变异，在SlVPE基因启动子区或基因下游开发了4个多态性分子标记。结论番茄SlVPE基因家族包含13个成员，其中11个成员以基因簇形式聚集于第8号染色体。SlVPE3和SlVPE5为组成型高表达基因，SlVPE2和SlVPE7在果实发育早期特异性高表达，而非生物胁迫主要诱导SlVPE3、SlVPE7和SlVPE8基因的表达。

关键词: 番茄, 液泡加工酶, 顺式作用元件, 非生物胁迫, 基因簇, 启动子, 分子标记, 醋栗番茄

Abstract:

Objective To systematically identify the members of vacuolar processing enzyme (VPE) gene family in tomato, and elucidate its evolutionary relationships, expression patterns, and potential functions in response to abiotic stress. Method Members of the SlVPE family were identified using bioinformatics methods. Systematic analyses were performed on their physicochemical properties, phylogenetic relationships, gene structures, conserved domains, chromosomal distribution, cis-acting elements, and interspecific collinearity. Public transcriptome data and RT-qPCR were integrated to analyze the tissue-specific expression patterns of the SlVPE family and their expression responses to drought, high/low temperature, salt, alkali, and combined salt-alkali stress. Result A total of 13 SlVPE genes containing both Peptidase_C13 and legumain_C domains were identified in tomato and classified into three subfamilies. With the exception of SlVPE4 and SlVPE5, all members were clustered in a gene cluster on chromosome 8. Expression analysis revealed significant tissue and spatiotemporal specificity within the SlVPE family: SlVPE3 and SlVPE5 were constitutively highly expressed, while SlVPE2 and SlVPE7 were fruit-specific highly expressed genes. Under abiotic stress, the family’s response was predominantly characterized by transcriptional suppression. Notably, SlVPE3 emerged as a core responsive gene to drought, salt, and combined salt-alkali stress, SlVPE7 was specifically induced by alkali stress, and SlVPE8 primarily responded to high and low-temperature stress. Based on sequence variations between wild tomato (Solanum pimpinellifolium) and cultivated tomato (S. lycopersicum), four polymorphic molecular markers were developed in the promoter regions or downstream regions of SlVPE gene. Conclusion The tomato SlVPE gene family consists of 13 members, 11 of which are clustered on chromosome 8. SlVPE3 and SlVPE5 are constitutively highly expressed genes, while SlVPE2 and SlVPE7 exhibit specific high expression during early fruit development. In contrast, abiotic stresses primarily induce the expressions of SlVPE3, SlVPE7, and SlVPE8.

Key words: tomato, vacuolar processing enzyme, cis-acting element, abiotic stress, gene cluster, promoter, molecular marker, Solanum pimpinellifolium

李迎辉, 王杨博涵, 周浩博, 卢心如, 张珂欣, 于洋, 李传友, 孙传龙. 番茄VPE基因家族鉴定和抗逆功能分析[J]. 生物技术通报, 2026, 42(3): 263-274.

LI Ying-hui, WANG Yang-bo-han, ZHOU Hao-bo, LU Xin-ru, ZHANG Ke-xin, YU Yang, LI Chuan-you, SUN Chuan-long. Identification of VPE Gene Family and Their Functional Analysis under Abiotic Stress in Tomato[J]. Biotechnology Bulletin, 2026, 42(3): 263-274.

图/表 8

表1 SlVPEs基本信息

Table 1 Basic information about SlVPEs

基因名称 Gene name	基因ID Gene ID	氨基酸数量 Number of amino acids	分子量 Molecular weight （kD）	疏水性 GRAVY	等电点 pI
SlVPE1	Solyc08g065790.2.1	460	51.77	-0.49	6.92
SlVPE2	Solyc08g065780.1.1	451	50.09	-0.12	5.76
SlVPE3	Solyc08g065610.2.1	470	52.11	-0.36	7.27
SlVPE4	Solyc08g079160.2.1	469	52.00	-0.33	7.59
SlVPE5	Solyc12g095910.1.1	463	51.04	-0.20	5.05
SlVPE6	Solyc08g065530.1.1	483	53.88	-0.31	5.83
SlVPE7	Solyc08g065570.1.1	428	47.54	-0.28	7.49
SlVPE8	Solyc08g065590.1.1	446	49.35	-0.30	7.26
SlVPE9	Solyc08g065690.1.1	450	49.50	-0.20	7.27
SlVPE10	Solyc08g065710.1.1	451	50.68	-0.44	7.78
SlVPE11	Solyc08g065720.1.1	482	53.22	-0.34	5.67
SlVPE12	Solyc08g065740.1.1	497	55.21	-0.37	5.49
SlVPE13	Solyc08g065750.1.1	480	52.97	-0.27	6.10

图1 番茄等物种VPEs蛋白系统进化分析

Fig. 1 Phylogenetic analysis of VPEs protein in tomato (Solanum lycopersicum) and other species

图2 SlVPEs蛋白基序、保守结构域和基因结构分析A：SlVPE蛋白系统发育树；B：SlVPE蛋白保守基序分析；C：SlVPE蛋白保守结构域分析，绿色和黄色分别代表Peptidase_C13结构域和legumain_C结构域；D：SlVPE基因结构分析；绿框代表CDS，黄框代表UTR，灰色线条代表内含子

Fig. 2 Motifs, conserved domains and gene structure analysis of SlVPE proteinA: Phylogenetic tree of SlVPE proteins. B: Analysis of conserved motifs in SlVPE proteins. C: Analysis of conserved domains of SlVPE proteins, with green and yellow boxes representing Peptidase_C13 and legumain_C domains, respectively. D: Analysis of SlVPE gene structures. CDS, UTRs, and introns are indicated by green boxes, yellow boxes, and gray lines, respectively

图3 SlVPE基因染色体定位、种间共线性和顺式作用元件分析A：SlVPE基因在染色体中的位置；B：SlVPE基因在番茄、拟南芥、马铃薯和花生基因组之间的共线性关系；灰色和蓝色分别代表基因组所有基因和VPE基因的共线性；C：SlVPEs启动子的顺式作用元件热图；D：SlVPEs启动子顺式作用元件的种类、位置和数量的可视化

Fig. 3 Analysis of chromosomal localization, interspecies collinearity, and cis-acting elements of SlVPE genesA: Chromosomal locations of the SlVPE genes. B: Collinear relationships of SlVPE genes among tomato, Arabidopsis, potato, and peanut genomes. Gray and blue lines indicate the collinearity of all genes and VPE genes, respectively. C: Heatmap of cis-acting elements in SlVPEs promoters. D: Visualization of the types, positions, and numbers of cis-acting elements in SlVPEs promoters

图4 SlVPE基因在番茄不同组织中的表达谱分析数据以4个生物学重复（n=4）的均值±标准误（SE）表示。不同小写字母表示差异显著（P<0.05）

Fig. 4 Expression profile analysis of SlVPE gene in different tissues of tomatoData are presented as mean ± SE from four biological replicates (n=4). Different lowercase letters indicate significant differences (P<0.05)

图5 SlVPE蛋白的互作网络预测图

Fig. 5 Predicted interaction network of SlVPE proteins

图6 逆境胁迫下SlVPE基因表达分析干旱胁迫：20% PEG6000；盐胁迫：150 mmol/L NaCl；碱胁迫：100 mmol/L NaHCO3；盐碱复合胁迫：60 mmol/L NaCl+60 mmol/L NaHCO3；低温胁迫：12 ℃；高温胁迫：38 ℃。取样时间点为胁迫处理后7 d。数据以3个生物学重复（n=3）的均值±标准误（SE）表示；每个生物学重复包含3个技术重复。*P<0.05，**P<0.01

Fig. 6 Expression analysis of SlVPE genes under various abiotic stressesDrought stress： 20% PEG6000； salt stress： 150 mmol/L NaCl； alkali stress： 100 mmol/L NaHCO₃； salt-alkali combined stress： 60 mmol/L NaCl+60 mmol/L NaHCO3； low-temperature stress： 12 ℃； high-temperature stress： 38 ℃. Samples were collected at 7 d after stress treatment. Data are presented as mean±SE of three biological replicates （n=3）， each with three technical replicates. *P<0.05， **P<0.01

图7 SlVPEs基因分子标记的多态性检测利用琼脂糖凝胶电泳检测SlVPE6启动子区（A）、SlVPE11基因下游（B）、SlVPE13基因启动子区（C）、SlVPE10基因启动子区（D）在醋栗番茄和栽培番茄间的多态性。泳道1-6：醋栗番茄种质，依次为LA0533、LA1375、LA1420、LA2873、LA4763、LA1589；泳道7-12：栽培番茄材料，依次为AC、M82、TS-418、Hawaii7996、MoneyMaker、Heinz1706

Fig. 7 Polymorphism detection of SlVPE gene molecular markersAgarose gel electrophoresis was used to examine polymorphisms between Solanum pimpinellifolium and cultivated tomato in the promoter region of SlVPE6 (A), the downstream region of SlVPE11 (B), the promoter region of SlVPE13 (C), and the promoter region of SlVPE10 (D). Lane 1-6: S. pimpinellifolium accessions, LA0533, LA1375, LA1420, LA2873, LA4763, and LA1589; lane 7-12: cultivated tomato materials, AC, M82, TS-418, Hawaii7996, MoneyMaker, and Heinz1706

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