凤梨薄荷SDR基因家族全基因组鉴定及表达分析

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

摘要/Abstract

摘要：

目的短链脱氢酶/还原酶（SDR）属于NADPH依赖性氧化还原酶超家族，是植物代谢研究中重要的基因家族。对凤梨薄荷（Mentha suaveolens ‘Variegata’）中SDR基因家族进行全基因组鉴定和分析，为解析SDR基因功能与薄荷醇生物合成研究提供理论依据。方法基于凤梨薄荷单倍型基因组数据，利用生物信息学方法鉴定凤梨薄荷SDR基因家族，并进行理化特性、保守基序、染色体定位等分析，结合转录联合代谢组数据将SDR基因与薄荷醇合成途径上重要基因及化合物进行共表达分析，以及RT-qPCR分析与单萜类化合物强烈正相关的MsSDR基因表达模式。结果共鉴定出142个MsSDRs基因不均匀分布在12条染色体上，编码232-765个氨基酸。系统发育分析将MsSDRs蛋白分为5种类型：经典型（C）、延伸型（E）、非经典型（A）、发散型（D）以及未知型（U）。此外，MsSDRs的启动子序列分析识别出与光响应和胁迫反应相关的顺式作用元件。基因表达图谱显示超过一半MsSDRs至少在一个组织中表达。共表达分析发现32个SDR基因与单萜类化合物呈现较强相关性，RT-qPCR结果与RNA-Seq数据趋势基本一致。结论对凤梨薄荷SDR基因家族的全面分析发现142个MsSDRs基因参与了凤梨薄荷生长发育的多个阶段，多个MsSDRs基因与薄荷醇生物合成途径上的单萜类化合物相关，推测其可能参与薄荷醇的生物合成。

关键词: 凤梨薄荷, SDR基因家族, 功能分析, 表达谱, 薄荷醇生物合成

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

吴娅, 姚润, 杨含婷, 刘微, 杨帅, 宋驰, 陈士林. 凤梨薄荷SDR基因家族全基因组鉴定及表达分析[J]. 生物技术通报, 2025, 41(5): 175-185.

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.

图/表 6

表1 MsSDR 基因 Ka/Ks 分析

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

图1 凤梨薄荷MsSDR基因的系统进化树

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

图2 凤梨薄荷 MsSDR蛋白保守基序分析

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

图3 凤梨薄荷MsSDR基因的染色体定位以及共线性分析A：染色体定位；B：共线性分析

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

图4 凤梨薄荷MsSDR基因的KEGG通路富集分析（A），GO富集分析（B）以及顺式作用元件预测统计（C）

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

图5 凤梨薄荷MsSDR基因的不同组织的表达分析A：凤梨薄荷SDR基因在不同组织的表达模式；B：共表达网络图，绿色代表正相关，黄色代表负相关；C：6个MsSDR基因在不同组织中的表达谱，图中误差线表示标准偏差

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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