Identification and Comparative Analysis of the StGAox Genes in Diploid and Tetraploid Potatoes

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

Abstract

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

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.

Figures/Tables 10

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

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

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

Fig. 3 Chromosome mapping of StGAox genes in six potatoes

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

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

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

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

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.

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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