Identification and Expression Pattern Analysis of Rosa roxburghii SOD Gene Family

doi:10.13560/j.cnki.biotech.bull.1985.2023-1138

Abstract

Abstract:

【Objective】Superoxide dismutase（SOD）is a natural scavenger of oxygen free radicals in plants, which plays a crucial role in protecting plants from environmental stress. The aim of this study is to investigate the role of SOD in response to drought stress in Rosa roxburghii and to provide a basis for further research on the function of the SOD gene family in Rosa roxburghii. 【Method】The SOD gene family of R. roxburghii was systematically identified and analyzed by bioinformatics method. The physicochemical properties, chromosome location, gene structure, subfamily evolution, cis-acting elements and WGCNA were comprehensively analyzed. Additionally, the expression pattern of the SOD gene family of R. roxburghii under drought stress was analyzed by RT-qPCR. 【Result】There was a total of nine members of SOD gene family in R. roxburghii, including four Cu/ZnSOD genes, three MnSOD genes, and two FeSOD genes. These genes were scattered across five chromosomes. The analysis of gene structure indicated that members within the same subfamily had similar motifs, but there were notable variations in the number and arrangement of introns/exons. Subfamily evolution analysis demonstrated that the MnSOD subfamily was the most primitive, with high conservation across all protein positions, followed by the FeSOD and Cu/ZnSOD subfamilies. The Cu/ZnSOD subfamily could be further divided into three subclasses due to significant sequence differences. Cis-element analysis revealed the involvement of the SOD gene family in various plant hormones, growth, and stress responses. Notably, the promoter region of RrCSD2 contained flavonoid biosynthetic elements（MBSI）. Transcriptome and WGCNA analysis further revealed that the genes of RrCSD2 module were significantly enriched in flavonoid and flavonol biosynthesis, as well as flavonoid biosynthesis and arachidonic acid metabolism, suggesting that RrCSD2 may be involved in flavonoid metabolism. RT-qPCR results showed that the expressions of RrMSD1 and RrMSD2 significantly decreased under drought stress, while the expressions of the other seven genes increased overall. Specifically, the expressions of RrCSD2 and RrCSD3 were significantly up-regulated. 【Conclusion】The SOD genes of R. roxburghii play a crucial role in drought stress response.

Key words: Rosa roxburghii, SOD gene, subfamily evolution, WGCNA analysis, drought stress

WEN Jie, DU Yuan-xin, WU An-bo, YANG Guang-rong, LU Min, AN Hua-ming, NAN Hong. Identification and Expression Pattern Analysis of Rosa roxburghii SOD Gene Family[J]. Biotechnology Bulletin, 2024, 40(5): 153-166.

Figures/Tables 13

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基因名称Gene name	基因ID Gene ID	上游引物Upstream primer（5'-3'）	下游引物Downstream primer（5'-3'）
RrCSD1	evm.model.Contig149.101	GATGGCCCAACTACTGTGACT	ACCGTTTGTTGTGTCACCAAG
RrCSD2	evm.model.Contig172.106	CTGTATTGCCAGAGCTACTGAC	TGCACCCAGAATCCTAACAAC
RrCSD3	evm.model.Contig255.128	CCGGTGATTTGGGTAACGTCACT	GTTCATGTCCACCTGCCAGTCGTC
RrCSD4	evm.model.Contig428.424	ACCCAAGAAGATGACGGTCCT	TCGTGTCACCAAACTCATGCAAG
RrMSD1	evm.model.Contig308.148	ATCATGGACCTCCATCACTT	GTGGAGGAGTCAACTGTATC
RrMSD2	evm.model.Contig308.149	GATACGGAAGGAGGAGGTGA	GAACCTTGCAAAGAAGCACC
RrMSD3	evm.model.Contig317.61	GCACCACCAGGCTTACATCACC	CGCTCTGCAACTTAACGACGG
RrFSD1	evm.model.Contig217.78	TGAAGCCTCCTCCGTATCCA	TATCCACATAACCCCTATGGTG
RrFSD2	evm.model.Contig285.37	AACCATCTTGTGTCTTGGAA	AACAGGGATATTAGGTTCGC
UBQ	-	ATGCAGATTTTGTGAAGAC	ACCACCACGRAGACGGAG

基因名称Gene name	基因ID Gene ID	上游引物Upstream primer（5'-3'）	下游引物Downstream primer（5'-3'）
RrCSD1	evm.model.Contig149.101	GATGGCCCAACTACTGTGACT	ACCGTTTGTTGTGTCACCAAG
RrCSD2	evm.model.Contig172.106	CTGTATTGCCAGAGCTACTGAC	TGCACCCAGAATCCTAACAAC
RrCSD3	evm.model.Contig255.128	CCGGTGATTTGGGTAACGTCACT	GTTCATGTCCACCTGCCAGTCGTC
RrCSD4	evm.model.Contig428.424	ACCCAAGAAGATGACGGTCCT	TCGTGTCACCAAACTCATGCAAG
RrMSD1	evm.model.Contig308.148	ATCATGGACCTCCATCACTT	GTGGAGGAGTCAACTGTATC
RrMSD2	evm.model.Contig308.149	GATACGGAAGGAGGAGGTGA	GAACCTTGCAAAGAAGCACC
RrMSD3	evm.model.Contig317.61	GCACCACCAGGCTTACATCACC	CGCTCTGCAACTTAACGACGG
RrFSD1	evm.model.Contig217.78	TGAAGCCTCCTCCGTATCCA	TATCCACATAACCCCTATGGTG
RrFSD2	evm.model.Contig285.37	AACCATCTTGTGTCTTGGAA	AACAGGGATATTAGGTTCGC
UBQ	-	ATGCAGATTTTGTGAAGAC	ACCACCACGRAGACGGAG

基因名称 Gene name	基因ID Gene ID	氨基酸 Amino acid/aa	分子量 Molecular weight/Da	等电点 pI	亚细胞定位 Location
RrCSD1	evm.model.Contig149.101	161	16 424.23	5.81	线粒体Mitochondria
RrCSD2	evm.model.Contig172.106	252	26 826.36	4.82	线粒体Mitochondria
RrCSD3	evm.model.Contig255.128	126	12 912.35	5.68	过氧化物酶体Peroxysome
RrCSD4	evm.model.Contig428.424	224	23 278.95	5.79	叶绿体Chloroplast
RrMSD1	evm.model.Contig308.148	196	21 612.59	7.73	线粒体Mitochondria
RrMSD2	evm.model.Contig308.149	235	26 494.16	6.16	线粒体Mitochondria
RrMSD3	evm.model.Contig317.61	180	19 243.86	7.07	线粒体Mitochondria
RrFSD1	evm.model.Contig217.78	268	30 684.68	5.43	线粒体Mitochondria
RrFSD2	evm.model.Contig285.37	270	31 123.38	6.33	线粒体Mitochondria

基因名称 Gene name	基因ID Gene ID	氨基酸 Amino acid/aa	分子量 Molecular weight/Da	等电点 pI	亚细胞定位 Location
RrCSD1	evm.model.Contig149.101	161	16 424.23	5.81	线粒体Mitochondria
RrCSD2	evm.model.Contig172.106	252	26 826.36	4.82	线粒体Mitochondria
RrCSD3	evm.model.Contig255.128	126	12 912.35	5.68	过氧化物酶体Peroxysome
RrCSD4	evm.model.Contig428.424	224	23 278.95	5.79	叶绿体Chloroplast
RrMSD1	evm.model.Contig308.148	196	21 612.59	7.73	线粒体Mitochondria
RrMSD2	evm.model.Contig308.149	235	26 494.16	6.16	线粒体Mitochondria
RrMSD3	evm.model.Contig317.61	180	19 243.86	7.07	线粒体Mitochondria
RrFSD1	evm.model.Contig217.78	268	30 684.68	5.43	线粒体Mitochondria
RrFSD2	evm.model.Contig285.37	270	31 123.38	6.33	线粒体Mitochondria

序号No.	基因ID Gene ID	物种Species	基因名称Gene name	分类Classifying
1	FvH4_6g04231.t2	野草莓F. vesca	FvSOD1	Cu/ZnSOD
2	FvH4_3g30620.t1		FvSOD2	Cu/ZnSOD
3	FvH4_1g28280.t1		FvSOD3	Cu/ZnSOD
4	FvH4_5g01090.t1		FvSOD4	Cu/ZnSOD
5	FvH4_7g25730.t1		FvSOD5	MnSOD
6	FvH4_4g37110.t1		FvSOD6	FeSOD
7	FvH4_7g26501.t1		FvSOD7	FeSOD
8	RchiOBHm_Chr3g0452901	月季R. chinensis	RcSOD1	Cu/ZnSOD
9	RchiOBHm_Chr5g0056701		RcSOD2	Cu/ZnSOD
10	RchiOBHm_Chr3g0496871		RcSOD3	Cu/ZnSOD
11	RchiOBHm_Chr2g0126391		RcSOD4	Cu/ZnSOD
12	RchiOBHm_Chr1g0371971		RcSOD5	MnSOD
13	RchiOBHm_Chr4g0446901		RcSOD6	FeSOD
14	RchiOBHm_Chr5g0072741		RcSOD7	MnSOD
15	RchiOBHm_Chr1g0373101		RcSOD8	FeSOD
16	RchiOBHm_Chr1g0318061		RcSOD9	FeSOD