Identification and bioinformatics analysis of superoxide dismutase gene in <i>Mangifera indica</i>

SHI Shaopu; ZHOU Kaibing

doi:10.15886/j.cnki.rdswxb.20240117

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Volume 15 Issue 6

Nov. 2024

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Article Navigation > Journal of Tropical Biology > 2024 > 15(6): 718-727

SHI Shaopu, ZHOU Kaibing. Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica[J]. Journal of Tropical Biology, 2024, 15(6): 718-727. doi: 10.15886/j.cnki.rdswxb.20240117

Citation:

SHI Shaopu, ZHOU Kaibing. Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica[J]. Journal of Tropical Biology, 2024, 15(6): 718-727. doi: 10.15886/j.cnki.rdswxb.20240117

Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica

doi: 10.15886/j.cnki.rdswxb.20240117

SHI Shaopu^1,2,
ZHOU Kaibing^{1,2
,
,}

1. School of Breeding and Multiplication/Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China;
2. School of Tropical Agriculture and Forestry/SARA/SRR, Hainan University, Haikou, Hainan 570228, China

Received Date: 2024-07-17
Rev Recd Date: 2024-09-23

Abstract

Superoxide dismutase（SOD） is an important enzyme in the plant antioxidant system, playing a crucial role in plant growth and development. An attempt was made to analyze the gene function of MiSOD and its expression patterns in different tissues and under enhanced UV-B irradiation. Members of the MiSOD gene family from multiple aspects such as protein characteristics, phylogenetic relationships, gene structure, and promoter cis acting elements were identified by using the mango genome and bioinformatics methods, and the expression patterns of MiSOD gene family members were identified by using the transcriptome analysis. A total of 10 SOD genes were identified in the mango fruit, and most of the MiSOD proteins belong to stable proteins and acidic proteins. The phylogenetic analysis of multiple species SOD proteins showed that SOD was clustered into three subgroups according to protein types. Gene structure analysis shows that the SOD gene contains 5-8introns, and genes from the same evolutionary branch have more similar structures. The conserved motifs and domains of their proteins are also the same. Ten MiSOD are distributed on 7 chromosomes and 1 fragment,containing 3 segmental duplication genes. The analysis of cis acting elements showed that the promoters of MiSOD members contain growth and development elements, hormone response elements, and stress response related elements. The expression pattern of MiSOD genes varies in different tissues of ‘Alphonso’ mango.MiCSD3, MiFSD1, 2, 3 have low expression levels in different tissues; the expression level of MiCSD4 is highest in the flesh, leaves, bark, and peel; the expression level of MiMSD1 is highest in the seeds, and the expression level of MiCSD1 is highest in the roots and flowers. Compared with the control, there was no significant difference in the MiSOD genes in the flesh of “Tainong-1” mango under enhanced UV-B irradiation. In summary, members of the MiSOD gene family may exert different functions by sensing different types of signals, thereby forming different expression patterns. SOD may not play a key role in the response of ‘Tainong-1’ mango to UV-B stress.This study lays the foundation for further investigating the response mechanism of MiSOD genes to different signals.
- mango,
- superoxide dismutase（SOD）,
- gene family,
- expression pattern

References

[1]	CRAMER G R, URANO K, DELROT S, et al. Effects of abiotic stress on plants:a systems biology perspective[J].BMC plant biology, 2011, 11:163.
[2]	KOPECKÁR, KAMENIAROVÁM,ČERNÝM, et al. Abiotic stress in crop production[J]. International Journal of Molecular Sciences, 2023, 24(7):6603.
[3]	MANSOOR S, ALI WANI O, LONE J K, et al. Reactive oxygen species in plants:from source to sink[J]. Antioxidants, 2022, 11(2):225.
[4]	ZULFIQAR F, ASHRAF M. Antioxidants as modulators of arsenic-induced oxidative stress tolerance in plants:an overview[J]. Journal of Hazardous Materials, 2022, 427:127891.
[5]	GECHEV T S, VAN BREUSEGEM F, STONE J M, et al.Reactive oxygen species as signals that modulate plant stress responses and programmed cell death[J]. BioEssays:News and Reviews in Molecular, Cellular and Developmental Biology, 2006, 28(11):1091-1101.
[6]	KERCHEV P I, VAN BREUSEGEM F. Improving oxidative stress resilience in plants[J]. The Plant Journal:for Cell and Molecular Biology, 2022, 109(2):359-372.
[7]	WANG Y, BRANICKY R, NOËA, et al. Superoxide dismutases:Dual roles in controlling ROS damage and regulating ROS signaling[J]. The Journal of Cell Biology, 2018,217(6):1915-1928.
[8]	ABREU I A, CABELLI D E. Superoxide dismutases-a review of the metal-associated mechanistic variations[J].Biochimica et Biophysica Acta, 2010, 1804(2):263-274.
[9]	SUTHERLAND K M, WARD L M, COLOMBERO C R,et al. Inter-domain horizontal gene transfer of nickelbinding superoxide dismutase[J]. Geobiology, 2021, 19(5):450-459.
[10]	MOHAMMADI M, TAVAKOLI A, POURYOUSEF M, et al. Study the effect of 24-epibrassinolide application on the Cu/Zn-SOD expression and tolerance to drought stress in common bean[J]. Physiology and Molecular Biology of Plants, 2020, 26(3):459-474.
[11]	ARABZADEH N, KHAVARI-NEJAD R A. Effect of drought stress on superoxide dismutase activity in two species of Haloxylon aphyllum and Haloxylon persicum[J].Pakistan Journal of Biological Sciences:PJBS, 2013,16(8):351-361.
[12]	FAIZE M, BURGOS L, FAIZE L, et al. Involvement of cytosolic ascorbate peroxidase and Cu/Zn-superoxide dismutase for improved tolerance against drought stress[J].Journal of Experimental Botany, 2011, 62(8):2599-2613.
[13]	ZHU Y, LUO X, NAWAZ G, et al. Physiological and Biochemical Responses of four cassava cultivars to drought stress[J]. Scientific Reports, 2020, 10:6968.
[14]	LI B, WANG W. Salicylic acid induces tolerance of Vitisriparia×V.labrusca to chilling stress by altered photosynthetic, antioxidant mechanisms and expression of cold stress responsive genes[J]. Plant Signaling&Behavior,2021, 16(11):1973711.
[15]	WU G, NIU X, CHEN J, et al. Hydrogen sulfide alleviates oxidative damage under chilling stress through mitogen-activated protein kinase in tomato[J]. Antioxidants, 2024, 13(3):323.
[16]	XU C, WANG Y, YANG H, et al. Cold acclimation alleviates photosynthetic inhibition and oxidative damage induced by cold stress in citrus seedlings[J]. Plant Signaling&Behavior, 2023, 18(1):2285169.
[17]	ZHANG L, TIAN W, HUANG G, et al. The SikCuZnSOD3 gene improves abiotic stress resistance in transgenic cotton[J]. Molecular Breeding, 2021, 41(3):26.
[18]	DIAZ-VIVANCOS P, FAIZE M, BARBA-ESPIN G, et al.Ectopic expression of cytosolic superoxide dismutase and ascorbate peroxidase leads to salt stress tolerance in transgenic plums[J]. Plant Biotechnology Journal, 2013,11(8):976-985.
[19]	SHAFI A, GILL T, SREENIVASULU Y, et al. Improved callus induction, shoot regeneration, and salt stress tolerance in Arabidopsis overexpressing superoxide dismutase from Potentilla atrosanguinea[J]. Protoplasma,2015, 252(1):41-51.
[20]	WARSCHEFSKY E J, VON WETTBERG E J B. Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication[J].The New Phytologist, 2019, 222(4):2023-2037.
[21]	ANSARI M W, BAINS G, SHUKLA A, et al. Low temperature stress ethylene and not Fusarium, might be responsible for mango malformation[J]. Plant Physiology and Biochemistry:PPB, 2013, 69:34-38.
[22]	LIU X, XIAO Y, ZI J, et al. Differential effects of low and high temperature stress on pollen germination and tube length of mango (Mangifera indica L.) genotypes[J]. Scientific Reports, 2023, 13:611.
[23]	HELALY M N, EL-HOSEINY H, EL-SHEERY N I, et al. Regulation and physiological role of silicon in alleviating drought stress of mango[J]. Plant Physiology and Biochemistry:PPB, 2017, 118:31-44.
[24]	YU W, KONG G, CHAO J, et al. Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress[J].Peer J, 2022, 10:e14251.
[25]	SONG J, ZENG L, CHEN R, et al. In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula[J]. 3 Biotech, 2018,8(8):348.
[26]	FENG K, YU J, CHENG Y, et al. The SOD gene family in tomato:identification, phylogenetic relationships, and expression patterns[J]. Frontiers in Plant Science, 2016,7:1279.
[27]	ZAMEER R, FATIMA K, AZEEM F, et al. Genome-wide characterization of superoxide dismutase (SOD) genes in daucus carota:novel insights into structure, expression,and binding interaction with hydrogen peroxide (H2O2) under abiotic stress condition[J]. Frontiers in Plant Science, 2022, 13:870241.
[28]	ZHOU C, ZHU C, FU H, et al. Genome-wide investigation of superoxide dismutase (SOD) gene family and their regulatory miRNAs reveal the involvement in abiotic stress and hormone response in tea plant (Camellia sinensis)[J]. PLoS One, 2019, 14(10):e0223609.
[29]	SU W, RAZA A, GAO A, et al. Genome-wide analysis and expression profile of superoxide dismutase (SOD) gene family in rapeseed (Brassica napus L.) under different hormones and abiotic stress conditions[J]. Antioxidants, 2021, 10(8):1182.
[30]	ROGOZIN I B, SVERDLOV A V, BABENKO V N, et al.Analysis of evolution of exon-intron structure of eukaryotic genes[J]. Briefings in bioinformatics, 2005, 6(2):118-134.
[31]	XU G, GUO C, SHAN H, et al. Divergence of duplicate genes in exon-intron structure[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(4):1187-1192.

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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

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Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica

1. School of Breeding and Multiplication/Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China;

2. School of Tropical Agriculture and Forestry/SARA/SRR, Hainan University, Haikou, Hainan 570228, China

Received Date: 2024-07-17

Rev Recd Date: 2024-09-23

Key words:

Abstract: Superoxide dismutase（SOD） is an important enzyme in the plant antioxidant system, playing a crucial role in plant growth and development. An attempt was made to analyze the gene function of MiSOD and its expression patterns in different tissues and under enhanced UV-B irradiation. Members of the MiSOD gene family from multiple aspects such as protein characteristics, phylogenetic relationships, gene structure, and promoter cis acting elements were identified by using the mango genome and bioinformatics methods, and the expression patterns of MiSOD gene family members were identified by using the transcriptome analysis. A total of 10 SOD genes were identified in the mango fruit, and most of the MiSOD proteins belong to stable proteins and acidic proteins. The phylogenetic analysis of multiple species SOD proteins showed that SOD was clustered into three subgroups according to protein types. Gene structure analysis shows that the SOD gene contains 5-8introns, and genes from the same evolutionary branch have more similar structures. The conserved motifs and domains of their proteins are also the same. Ten MiSOD are distributed on 7 chromosomes and 1 fragment,containing 3 segmental duplication genes. The analysis of cis acting elements showed that the promoters of MiSOD members contain growth and development elements, hormone response elements, and stress response related elements. The expression pattern of MiSOD genes varies in different tissues of ‘Alphonso’ mango.MiCSD3, MiFSD1, 2, 3 have low expression levels in different tissues; the expression level of MiCSD4 is highest in the flesh, leaves, bark, and peel; the expression level of MiMSD1 is highest in the seeds, and the expression level of MiCSD1 is highest in the roots and flowers. Compared with the control, there was no significant difference in the MiSOD genes in the flesh of “Tainong-1” mango under enhanced UV-B irradiation. In summary, members of the MiSOD gene family may exert different functions by sensing different types of signals, thereby forming different expression patterns. SOD may not play a key role in the response of ‘Tainong-1’ mango to UV-B stress.This study lays the foundation for further investigating the response mechanism of MiSOD genes to different signals.

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Reference (31)

[1]	CRAMER G R, URANO K, DELROT S, et al. Effects of abiotic stress on plants:a systems biology perspective[J].BMC plant biology, 2011, 11:163.
[2]	KOPECKÁR, KAMENIAROVÁM,ČERNÝM, et al. Abiotic stress in crop production[J]. International Journal of Molecular Sciences, 2023, 24(7):6603.
[3]	MANSOOR S, ALI WANI O, LONE J K, et al. Reactive oxygen species in plants:from source to sink[J]. Antioxidants, 2022, 11(2):225.
[4]	ZULFIQAR F, ASHRAF M. Antioxidants as modulators of arsenic-induced oxidative stress tolerance in plants:an overview[J]. Journal of Hazardous Materials, 2022, 427:127891.
[5]	GECHEV T S, VAN BREUSEGEM F, STONE J M, et al.Reactive oxygen species as signals that modulate plant stress responses and programmed cell death[J]. BioEssays:News and Reviews in Molecular, Cellular and Developmental Biology, 2006, 28(11):1091-1101.
[6]	KERCHEV P I, VAN BREUSEGEM F. Improving oxidative stress resilience in plants[J]. The Plant Journal:for Cell and Molecular Biology, 2022, 109(2):359-372.
[7]	WANG Y, BRANICKY R, NOËA, et al. Superoxide dismutases:Dual roles in controlling ROS damage and regulating ROS signaling[J]. The Journal of Cell Biology, 2018,217(6):1915-1928.
[8]	ABREU I A, CABELLI D E. Superoxide dismutases-a review of the metal-associated mechanistic variations[J].Biochimica et Biophysica Acta, 2010, 1804(2):263-274.
[9]	SUTHERLAND K M, WARD L M, COLOMBERO C R,et al. Inter-domain horizontal gene transfer of nickelbinding superoxide dismutase[J]. Geobiology, 2021, 19(5):450-459.
[10]	MOHAMMADI M, TAVAKOLI A, POURYOUSEF M, et al. Study the effect of 24-epibrassinolide application on the Cu/Zn-SOD expression and tolerance to drought stress in common bean[J]. Physiology and Molecular Biology of Plants, 2020, 26(3):459-474.
[11]	ARABZADEH N, KHAVARI-NEJAD R A. Effect of drought stress on superoxide dismutase activity in two species of Haloxylon aphyllum and Haloxylon persicum[J].Pakistan Journal of Biological Sciences:PJBS, 2013,16(8):351-361.
[12]	FAIZE M, BURGOS L, FAIZE L, et al. Involvement of cytosolic ascorbate peroxidase and Cu/Zn-superoxide dismutase for improved tolerance against drought stress[J].Journal of Experimental Botany, 2011, 62(8):2599-2613.
[13]	ZHU Y, LUO X, NAWAZ G, et al. Physiological and Biochemical Responses of four cassava cultivars to drought stress[J]. Scientific Reports, 2020, 10:6968.
[14]	LI B, WANG W. Salicylic acid induces tolerance of Vitisriparia×V.labrusca to chilling stress by altered photosynthetic, antioxidant mechanisms and expression of cold stress responsive genes[J]. Plant Signaling&Behavior,2021, 16(11):1973711.
[15]	WU G, NIU X, CHEN J, et al. Hydrogen sulfide alleviates oxidative damage under chilling stress through mitogen-activated protein kinase in tomato[J]. Antioxidants, 2024, 13(3):323.
[16]	XU C, WANG Y, YANG H, et al. Cold acclimation alleviates photosynthetic inhibition and oxidative damage induced by cold stress in citrus seedlings[J]. Plant Signaling&Behavior, 2023, 18(1):2285169.
[17]	ZHANG L, TIAN W, HUANG G, et al. The SikCuZnSOD3 gene improves abiotic stress resistance in transgenic cotton[J]. Molecular Breeding, 2021, 41(3):26.
[18]	DIAZ-VIVANCOS P, FAIZE M, BARBA-ESPIN G, et al.Ectopic expression of cytosolic superoxide dismutase and ascorbate peroxidase leads to salt stress tolerance in transgenic plums[J]. Plant Biotechnology Journal, 2013,11(8):976-985.
[19]	SHAFI A, GILL T, SREENIVASULU Y, et al. Improved callus induction, shoot regeneration, and salt stress tolerance in Arabidopsis overexpressing superoxide dismutase from Potentilla atrosanguinea[J]. Protoplasma,2015, 252(1):41-51.
[20]	WARSCHEFSKY E J, VON WETTBERG E J B. Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication[J].The New Phytologist, 2019, 222(4):2023-2037.
[21]	ANSARI M W, BAINS G, SHUKLA A, et al. Low temperature stress ethylene and not Fusarium, might be responsible for mango malformation[J]. Plant Physiology and Biochemistry:PPB, 2013, 69:34-38.
[22]	LIU X, XIAO Y, ZI J, et al. Differential effects of low and high temperature stress on pollen germination and tube length of mango (Mangifera indica L.) genotypes[J]. Scientific Reports, 2023, 13:611.
[23]	HELALY M N, EL-HOSEINY H, EL-SHEERY N I, et al. Regulation and physiological role of silicon in alleviating drought stress of mango[J]. Plant Physiology and Biochemistry:PPB, 2017, 118:31-44.
[24]	YU W, KONG G, CHAO J, et al. Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress[J].Peer J, 2022, 10:e14251.
[25]	SONG J, ZENG L, CHEN R, et al. In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula[J]. 3 Biotech, 2018,8(8):348.
[26]	FENG K, YU J, CHENG Y, et al. The SOD gene family in tomato:identification, phylogenetic relationships, and expression patterns[J]. Frontiers in Plant Science, 2016,7:1279.
[27]	ZAMEER R, FATIMA K, AZEEM F, et al. Genome-wide characterization of superoxide dismutase (SOD) genes in daucus carota:novel insights into structure, expression,and binding interaction with hydrogen peroxide (H2O2) under abiotic stress condition[J]. Frontiers in Plant Science, 2022, 13:870241.
[28]	ZHOU C, ZHU C, FU H, et al. Genome-wide investigation of superoxide dismutase (SOD) gene family and their regulatory miRNAs reveal the involvement in abiotic stress and hormone response in tea plant (Camellia sinensis)[J]. PLoS One, 2019, 14(10):e0223609.
[29]	SU W, RAZA A, GAO A, et al. Genome-wide analysis and expression profile of superoxide dismutase (SOD) gene family in rapeseed (Brassica napus L.) under different hormones and abiotic stress conditions[J]. Antioxidants, 2021, 10(8):1182.
[30]	ROGOZIN I B, SVERDLOV A V, BABENKO V N, et al.Analysis of evolution of exon-intron structure of eukaryotic genes[J]. Briefings in bioinformatics, 2005, 6(2):118-134.
[31]	XU G, GUO C, SHAN H, et al. Divergence of duplicate genes in exon-intron structure[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(4):1187-1192.

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Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica

doi: 10.15886/j.cnki.rdswxb.20240117

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References

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通讯作者: 陈斌, bchen63@163.com

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Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica

doi: 10.15886/j.cnki.rdswxb.20240117

1. School of Breeding and Multiplication/Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China;

2. School of Tropical Agriculture and Forestry/SARA/SRR, Hainan University, Haikou, Hainan 570228, China

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Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica

doi: 10.15886/j.cnki.rdswxb.20240117

Abstract

References

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通讯作者: 陈斌, bchen63@163.com

Proportional views

Related

Identification and bioinformatics analysis of superoxide dismutase gene in Mangifera indica

doi: 10.15886/j.cnki.rdswxb.20240117

1. School of Breeding and Multiplication/Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China; 2. School of Tropical Agriculture and Forestry/SARA/SRR, Hainan University, Haikou, Hainan 570228, China

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1. School of Breeding and Multiplication/Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, Hainan 572025, China;

2. School of Tropical Agriculture and Forestry/SARA/SRR, Hainan University, Haikou, Hainan 570228, China