Genome-wide Identification and Expression Analysis of SDR Gene Family in Mentha suaveolens ‘Variegata’

doi:10.13560/j.cnki.biotech.bull.1985.2024-0997

Abstract

Abstract:

Objective Short-chain dehydrogenases/reductases (SDRs), belong to the NADPH-dependent oxidoreductase superfamily, represent an important gene family in plant metabolism. This study conducted a comprehensive identification and analysis of the SDR gene family in Mentha suaveolens 'Variegata', providing a theoretical basis for understanding the functions of SDR genes and their roles in menthol biosynthesis. Method Based on the genome data of M. suaveolens haplotype, bioinformatics methods were employed to identify the SDR gene family, and to analyze their physicochemical properties, conserved motifs, and chromosomal localization. Co-expression analysis was performed between SDR genes and important monoterpene compounds on the menthol synthesis pathway based on transcriptome and metabolome data. Additionally, RT-qPCR was performed to analyze expression patterns of MsSDR genes strongly correlated with monoterpene compounds. Result Total 142 MsSDR genes were identified in M. suaveolens, unevenly distributed across 12 chromosomes, encoding 232 to 765 amino acids. Phylogenetic analysis categorized MsSDR proteins into five types: classical (C), extended (E), non-classical (A), divergent (D)and unknown (U). Additionally, promoter sequence analysis of MsSDR identified the cis-acting elements associated with photo-response and stress responses. Gene expression profiles indicated that more than half of the MsSDRs were expressed in at least one tissue. Co-expression analysis revealed that 32 SDR genes presented a strong correlation with monoterpene compounds. Conclusion A comprehensive analysis of the M. suaveolensSDR gene family found that 142 MsSDRs genes were involved in multiple stages of its growth and development. Multiple MsSDRs were associated with monoterpene compounds in the menthol biosynthesis pathway, suggesting their potential involvement in menthol biosynthesis.

Key words: Mentha suaveolens ‘Variegata’, SDR genes family, functional analysis, expression profile, menthol biosynthesis

WU Ya, YAO Run, YANG Han-ting, LIU Wei, YANG Shuai, SONG Chi, CHEN Shi-lin. Genome-wide Identification and Expression Analysis of SDR Gene Family in Mentha suaveolens ‘Variegata’[J]. Biotechnology Bulletin, 2025, 41(5): 175-185.

Figures/Tables 6

Table 1 Ka/Ks analysis of MsSDR genes

基因1 Gene 1	基因1 Gene 2	非同义替换率 Ka	同义替换率 Ks	Ka/Ks
MsSDR1E1	MsSDR1E3	0.08	1.16	0.07
MsSDR2E2	MsSDR2E3	0.07	1.30	0.05
MsSDR31E3	MsSDR31E2	0.17	0.66	0.25
MsSDR50E4	MsSDR50E5	0.23	2.21	0.10
MsSDR50E2	MsSDR50E7	0.07	0.46	0.16
MsSDR67E1	MsSDR67E2	0.05	0.78	0.06
MsSDR93E1	MsSDR93E2	0.03	1.69	0.02
MsSDR117E1	MsSDR117E3	0.28	1.70	0.17
MsSDR367E1	MsSDR367E2	0.11	1.22	0.09
MsSDR132C6	MsSDR132C1	0.29	3.11	0.09
MsSDR152C2	MsSDR152C1	0.13	0.89	0.15
MsSDR119C3	MsSDR119C2	0.11	2.87	0.04
MsSDR114C10	MsSDR114C12	0.19	1.99	0.10
MsSDR110C15	MsSDR110C8	0.42	0.73	0.58

Fig. 1 Phylogenetic tree of the MsSDRs of M. suaveolens

Fig. 2 Analysis of conserved motifs of MsSDR proteins in M. suaveolens

Fig. 3 Chromosomal localization of the MsSDRs in M. suaveolens and analysis of collinearityA: Localization of chromosomes. B: Colinearity analysis

Fig. 4 KEGG pathway enrichment analysis (A), GO enrichment analysis(B), and cis-acting element prediction statistics (C) for the MsSDRs gene in M. suaveolens

Fig. 5 Expression analysis of MsSDRs in different tissues of M. suaveolensA: Expression patterns of SDR genes in different tissues of M. suaveolens. B: Co-expression network diagram, with green representing positive correlation and yellow representing negative correlation. C: Expression profiles of six MsSDR genes in various tissues. The error line in the figure refers to the standard deviation

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