二倍体和四倍体马铃薯StGAox基因鉴定与比较分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-1018

摘要/Abstract

摘要：

目的赤霉素氧化酶GAox包括GA20氧化酶（GA20ox）、GA2氧化酶（GA2ox）和GA3氧化酶（GA3ox），是植物体内赤霉素GA生物合成的关键调控酶，与植物的生长发育及对胁迫的响应息息相关。从二倍体和四倍体马铃薯全基因组中鉴定StGAox基因家族成员，比较分析不同倍性的马铃薯中该基因家族的进化模式，为马铃薯StGAox的基因功能研究提供线索。方法基于3个二倍体和3个四倍体马铃薯全基因组信息，利用生物信息学方法对StGAox基因家族进行鉴定，比较分析不同倍性的马铃薯中该家族成员的系统发育关系、基因结构、染色体定位、共线性关系、基因复制模式、亚细胞定位、顺式作用元件、匍匐茎中的表达模式。结果二倍体马铃薯Solanum tuberosum group Phureja DM1-3 516 R44（DM）、S. chacoense M6（M6）和S. tuberosum group Tuberosum RH89-039-16（RH）分别鉴定到35、26和56个GAox同源基因，四倍体马铃薯品种大西洋（cv. Atlantic，Atl）、合作88（cv. Cooperation-88，C88）和cv. Otava（Ot）分别鉴定到99、133和105个同源基因，在12或24或48条染色体上呈不均匀分布，其编码蛋白主要定位于细胞核、细胞骨架及叶绿体中；通过对二倍体和四倍体马铃薯、番茄和拟南芥的比较进化分析将其分为3个亚族GA20ox、GA3ox和GA2ox，同一亚族具有相似的蛋白保守基序和基因结构；共线性分析发现6种马铃薯StGAox存在不同程度的易位；在基因复制方面，与二倍体马铃薯DM比较，四倍体马铃薯Atl、C88和Ot中分别有72、117、95个StGAox基因属于共线性基因，二倍体马铃薯M6和RH中分别有21和51个共线性基因；顺式元件分析表明，胁迫相关的CAAT-box、植物生长发育相关的TATA-box、植物激素相关的CGTCA-motif、ERE和TGACG-motif、光反应相关的Box 4和G-box的数量最多；StGAox在匍匐茎中表达模式不同，大多数StGAox基因TPM值均小于20，31个StGAox基因仅在膨大匍匐茎中有表达，12个基因在膨大匍匐茎中的表达量明显高于顶端弯钩状匍匐茎。结论二倍体和四倍体马铃薯中共鉴定到454个GAox基因，揭示了不同倍性的马铃薯GAox家族基因结构、基序组成、染色体分布、基因复制模式和匍匐茎中的表达谱。

关键词: 马铃薯, 倍性, 赤霉素氧化酶, 生物信息学分析, 基因复制

Abstract:

Objective Gibberellin oxidases (GAoxs), including GA20 oxidase (GA20ox), GA2 oxidase (GA2ox), and GA3 oxidase (GA3ox), are key regulatory enzymes in the biosynthesis of gibberellin (GA) in plants, playing crucial roles in plant growth, development, and stress responses. This study is aimed to identify members of the the StGAox gene family from the whole genomes of diploid and tetraploid potatoes, and to conduct a compareative analysis of the evolutionary patterns of this gene family in potatoes with different ploidy levels, providing insights into the potential functions of StGAox in potatoes. Method Based on the whole genome information of three diploid and three tetraploid potatoes, bioinformatics methods were used to identify and the StGAox gene family and comparatively analyze the phylogenetic relationships, gene structure, chromosome localization, collinearity, gene replication patterns, subcellular localization, cis-acting elements, and expression patterns in stolons for members of this family in potatoes with different ploidy levels. Result A total of 35, 26, and 56 GAox homologous genes were identified in the diploid potatoe Solanum tuberosum group Phureja DM1-3 516 R44 (DM), S. chacoense M6 (M6), and S. tuberosum group Tuberosum RH89-039-16 (RH), respectively. In tetraploid potato varieties, S. tuberosum cv. Atlantic (Atl), S. tuberosum cv. Cooperation-88 (C88), and S. tuberosum cv. Otava (Ot), 99, 133, and 105 homologous genes were identified, respectively. These genes were unevenly distributed on 12, 24, or 48 chromosomes, with their encoded proteins mainly located in the nucleus, cytoskeleton, and chloroplasts. By comparative evolutionary analysis between diploid and tetraploid potatoes, as well as tomatoes and Arabidopsis, the genes were classified into three subfamilies: GA20ox, GA3ox,and GA2ox, with similar conserved protein motifs and gene structures. Collinearity analysis revealed varying degrees of translocation in the StGAox among the six potatoes. In terms of gene replication, compared with diploid potato DM, 21 and 51 collinear genes were found in the diploid potatoes M6 and RH, respectively, while 72, 117, and 95 StGAox genes in the tetraploid potatoes Atl, C88, and Ot, respectively, were identified as collinear genes. Cis-regulatory element analysis showed that stress-related CAAT-box, growth-related TATA-box, hormone-related CGTCA-motif, ERE and TGACG-motif, and light-response elements such as Box 4 and G-boxes were the most abundant. Expression patterns analysis indicated that differential expression of StGAox in stolons, with most having TPM values below 20. Additionaly, 31 StGAox genes were exclusively expressed in swollen stolons, while 12 genes had significantly higher expressions in swollen stolons compared to the apical hooked stolons. Conclusion A total of 454 GAox genes are identified in diploid and tetraploid potatoes, revealing the gene structure, motif composition, chromosome distribution, gene replication patterns, and expression profiles of the GAox family in stolons with different ploidy levels.

Key words: potato, ploidy, gibberellin oxidase, bioinformatics analysis, gene replication

覃悦, 杨妍, 张磊, 卢丽丽, 李先平, 蒋伟. 二倍体和四倍体马铃薯StGAox基因鉴定与比较分析[J]. 生物技术通报, 2025, 41(3): 146-160.

QIN Yue, YANG Yan, ZHANG Lei, LU Li-li, LI Xian-ping, JIANG Wei. Identification and Comparative Analysis of the StGAox Genes in Diploid and Tetraploid Potatoes[J]. Biotechnology Bulletin, 2025, 41(3): 146-160.

图/表 10

图1 两种类型匍匐茎形态白线左侧为亚顶端未膨大的匍匐茎，将形成新的分枝；白线右侧为亚顶端膨大的匍匐茎，将形成试管薯

Fig. 1 Two types of stolon morphologyThe stolons on the left side of the white line are a subapical non-swollen stolon, which will form a new branch; the stolons on the right side of the white line are subapical swollen stolons, which will develop into microtubers

表1 二倍体和四倍体马铃薯信息及鉴定的GAox同源基因

Table 1 Information of diploid and tetraploid potatoes and identified of GAox homologous genes

序号 Number	名称 Name	简称 Abbreviation	倍性 Ploidy	染色体数量 Chromosome number	基因组版本 Genome version	StGA20ox	StGA3ox	StGA2ox	总数 Total
1	S. tuberosum group Phureja DM1-3 516 R44	DM	二倍体 Diploid	24	v6.1	15	7	13	35
2	S. chacoense M6	M6	二倍体 Diploid	24	v5.0	7	6	13	26
3	S. tuberosum group Tuberosum RH89-039-16	RH	二倍体 Diploid	24	v1.0	23	11	22	56
4	大西洋S. tuberosum cv. Atlantic	Atl	四倍体 Tetraploid	48	v3.0	46	9	44	99
5	合作88S. tuberosum cv. Cooperation-88	C88	四倍体 Tetraploid	48	v1.0	60	27	46	133
6	S. tuberosum cv. Otava	Ot	四倍体 Tetraploid	48	v1.0	39	26	40	105

图2 马铃薯StGAox基因家族成员进化关系及其保守结构域环形图由内向外依次表示为：赤霉素GAox家族成员的分类；6个马铃薯、番茄和拟南芥赤霉素GAox家族成员在进化关系上的分布；赤霉素GAox家族成员的保守结构域。PSSM-ID 177816、215142、215156、215404、215534、425547、442714、450120和464110分别指赤霉素2氧化酶相关的超家族cl31834、赤霉素3氧化酶相关的超家族cl33443、赤霉素20氧化酶相关的超家族cl33448、2OG-Fe（Ⅱ）加氧酶家族蛋白、2OG-Fe（Ⅱ）加氧酶家族蛋白相关的超家族cl33617、核糖体蛋白、双加氧酶相关结构域、脱氢酶（MDR）和吗啡合成N-末端非血红素双加氧酶

Fig. 2 Phylogenetic tree and conserved structural domains of potato StGAox gene family membersThe circular diagram indicates, from the inside out, the classification of the GAox gene family. The phylogentic relationships of the 6 GAox gene family members from potatoes, tomatoes, and Arabidopsis thaliana. Conservative domains of GAox gene family. PSSM-IDs 177816, 215142, 215156, 215404, 215534, 425547, 442714, 450120, and 464110 respectively refer to the gibberellin 2-oxidase-related superfamily cl31834, gibberellin 3-oxidase-related superfamily cl33443, gibberellin 20-oxidase-related superfamily cl33448, 2OG-Fe(‍Ⅱ) oxygenase family proteins, 2OG-Fe(‍Ⅱ) oxygenase family protein-related superfamily cl33617, ribosomal proteins, dioxygenase-related domains, dehydrogenase (MDR), and morphinan synthesis N-terminal non-heme dioxygenase

图3 六种马铃薯的StGAox基因染色体定位

Fig. 3 Chromosome mapping of StGAox genes in six potatoes

图4 马铃薯StGAox基因家族成员共线性分析A： 6个马铃薯基因组的谱系关系；B： 6个马铃薯基因组共线性分析

Fig. 4 Collinearity analysis of StGAox gene family membersA: Phylogenetic relationships of 6 potato genomes. B: Collinearity analysis of 6 potato genomes

图5 马铃薯StGAox基因家族成员编码蛋白理化性质分析

Fig. 5 Physicochemical property analysis of the proteins encoded by the StGAox gene family members in potatoes

图6 马铃薯StGAox基因家族成员Motif分析

Fig. 6 Motifs analysis of StGAox gene family members in potatoes

图7 StGAox基因家族成员密码子使用偏向性分析A： StGAox基因家族成员密码子相关性分析；B： StGAox基因家族成员密码子使用偏向性分析

Fig. 7 Analysis of codon usage bias in StGAox gene family membersA: Correlation analysis of codons among members of the StGAox gene family. B: Bias analysis of codon usage among members of the StGAox gene family

图8 StGAox基因家族成员顺式作用元件分析及亚细胞定位A： StGAox基因家族成员顺式作用元件分析；B： StGAox基因家族成员亚细胞定位分析

Fig. 8 Analysis of cis acting elements and subcellular localization of StGAox gene family membersA: Cis-acting element analysis of the StGAox gene family members. B. Subcellular localization analysis of the StGAox gene family members.

图9 StGAox基因家族成员表达量分析星号表示在匍匐茎中表达的StGAox基因，除14表示的节点外，其余数字标注的节点为6种马铃薯的StGAox同源基因，其中4-StGA3ox2、5-StGA3ox1、6-StGA3ox3、11-StGA2ox1、17-StGA20ox2、18-StGA20ox3、19-StGA20ox1代表已报道的StGAox基因

Fig. 9 Analysis of expressions of StGAox gene family membersThe asterisks indicate the expressions of the StGAox genes in stolons. Except for node 14, the other numbered nodes refer to the StGAox homologous genes in six potatoes. Specifically, 4-StGA3ox2, 5-StGA3ox1, 6-StGA3ox3, 11-StGA2ox1, 17-StGA20ox2, 18-StGA20ox3, and 19-StGA20ox1 refer to previously reported StGAox genes

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