西南农业学报2025，Vol.38Issue(9)：1822-1831,10.DOI:10.16213/j.cnki.scjas.2025.9.002
鼓槌石斛SBP基因家族全基因组鉴定与生物信息学分析
Genome-wide identification and bioinformatics analysis of SBP gene family in Dendrobium chrysotoxum
摘要
Abstract
[Objective]The study aimed to identify and analyze the SBP transcription factor family within the entire genome of Dendrobium chrysotoxum,which provided a solid foundation for further in-depth investigations into the biological functions of SBP transcription factors.[Method]Using bioinformatics methods,members of the SBP gene family were screened and identified from the whole genome of D.chrysotox-um.Systematic analyses were conducted on their protein physicochemical properties,subcellular localization,protein spatial structure,protein phosphorylation modification sites,chromosome localization,conserved domains and motifs,phylogenetic trees,and cis-acting elements in pro-moters.[Result]15 SBP genes were identified in the genome of D.chrysotoxum,which were unevenly distributed across 10 chromosomes.The number of amino acids ranged from 219 to 1086 aa,the isoelectric points ranged from 5.37 to 9.63,relative molecular masses ranged from 24 480.53 to 119 978.42 Da,instability indices ranged from 44.54 to 74.10,aliphatic indices were 52.65 to 81.42,and the grand average of hydropathicity(GRAVY)values was-0.787 to 0.575.Subcellular localization prediction indicated that 3 genes family members were lo-calized in the cytoplasm,while 15 genes were located in the nucleus.The secondary structure of the protein was mainly composed of regular α-helices and loose random coils,while the overall similarity of the tertiary structure was low and the spatial conformation was more complex.The number of protein phosphorylation modification sites ranged from 21 to 134.All family members possessed a highly conserved SBP do-main,which was composed of two zinc finger structural modules and a nuclear localization signal sequence.Different members of the SBP gene family contained distinct motifs,and genes with closer clustering relationships had similar motifs with the number of motifs ranging from 2 to 7.A total of 51 SBP proteins from D.chrysotoxum,Arabidopsis thaliana,and Oryza sativa were classified into 11 subfamilies,and 15 D.chrysotoxum SBP proteins were distributed in 8 subfamilies.A total of 22 types of cis-acting elements were identified in the promoter region of SBP genes,covering those involved in light response,hormone response and stress adversity response.SBP genes showed relatively low expres-sion levels in roots and stems but higher levels in leaves and flowers,and genes within the same subfamily exhibited similar expression pat-terns.[Conclusion]Members of the SBP gene family show significant differences in physicochemical properties and are classified into 8 phy-logenetic subfamilies.The structural domains and motifs within the same subfamily exhibit extremely strong conservativeness.The promoter re-gions mainly contain cis-acting elements involved in light response,hormone response,and stress response.SBP genes show differential expression in different tissues,potentially playing important roles in the growth and development of leaves and floral organs in D.chrysotoxum.关键词
鼓槌石斛/SBP/基因家族/生物信息学/保守结构域Key words
Dendrobium chrysotoxum/SBP/Gene family/Bioinformatics/Conservative domain分类
农业科技引用本文复制引用
董蓉娇,李泽生,姚志军,贾敏,罗凯,高燕,李桂琳..鼓槌石斛SBP基因家族全基因组鉴定与生物信息学分析[J].西南农业学报,2025,38(9):1822-1831,10.基金项目
云南省科技人才与平台计划-院士专家工作站(202405AF140026) （202405AF140026）
云南省热带作物科技创新体系建设子项目(DTARI-2025-03,DTARI-JJ2024-01) （DTARI-2025-03,DTARI-JJ2024-01）
德宏州"英才兴边计划"技术创新人才(2024RC006) （2024RC006）
