热带作物学报2025，Vol.46Issue(10)：2299-2313,15.DOI:10.3969/j.issn.1000-2561.2025.10.002
木薯AT-hook基序核定位基因家族的全基因组鉴定、表达谱及调控网络分析
Genome-wide Identification,Expression Profiling and Network Analysis of AT-hook Gene Family in Cassava
摘要
Abstract
The AT-hook Motif Nuclear Localized(AHL)protein family is known for its pivotal roles in plant growth regulation,developmental patterning,and stress signal transduction.Although the gene family has been studied in vari-ous plant species,the genomic characteristics,evolutionary mechanism,and expression profiles of the AHL family in cassava(Manihot esculenta)remain unexplored.In this study,we comprehensively investigated the evolutionary fea-tures and biological response of the MeAHL gene family through genome-wide identification,phylogenetic analysis,structural characterization,and large-scale transcriptomes based on the cassava SC205 reference genome.We identified 41 putative members through genome-wide identification.Physicochemical property analysis showed that all 41 MeAHLs were hydrophilic proteins,and 40 of them were unstable proteins,with the number of amino acids generally ranging from 188 to 446 aa.Phylogenetic analysis indicated that the MeAHL family members could be divided into two clades,Clade A and Clade B.Two MeAHL gene clusters were located in the distal telomeric regions of chromosomes Chr01 and Chr02,respectively.Replication type analysis revealed that the evolution of MeAHLs was mainly driven by whole-genome duplication(WGD)and dispersed duplication(DSD),with the Ka/Ks values＜1.Evolutionary mecha-nism analysis indicated that whole-genome duplication(WGD)primarily drove the MeAHL gene family expansion.Gene structure analysis showed that MeAHL genes were mainly composed of 1-10 exons.Analysis of conserved do-mains and motifs showed that all MeAHLs had the PPC/DUF296 domain and AT-hook motif.Members of Clade A gen-erally contained one Type-Ⅰ AT-hook motif.Among members of Clade B,except for SC20508G13380 and SC20509G13950,which contained one Type-Ⅱ AT-hook motif,most members contained two AT-hooks(Type-Ⅰ and Type-Ⅱ).Cis-acting element analysis via PlantCARE showed that the cis-acting elements related to light response were the most abundant in MeAHLs,such as Box 4,G-box,and they also contained elements responsive to hormones,biotic stresses,and abiotic stresses,such as ABRE,MBS,W-box,and TC-rich repeats.Tissue-specific expression profiling revealed distinct expression patterns between two clades of MeAHL across 11 different tissues.Stress transcriptome analysis demonstrated significant responses of specific MeAHLs to drought(ABA/PEG treatments),cassava bacterial blight(Xanthomonas axonopodis pv.manihotis),and mite infestation,showing clade-specific regulatory patterns.Pro-tein-protein interaction(PPI)network prediction suggested some MeAHLs formed functional modules with bHLH,NAC,ARF,and NB-LRR proteins involved in plant development and stress responses.This study would provide the system-atic characterization of AHL family evolution and functional diversification in cassava,offering theoretical foundations for molecular breeding applications.关键词
木薯/AHL基因家族/生物信息学分析/表达分析/调控网络Key words
cassava/AHL gene family/bioinformatics analysis/expression analysis/protein-protein interaction(PPI)network分类
农业科技引用本文复制引用
王雨,郑芸霏,赵海旭,李美英,谢郑楠,叶晓雪,纪长绵,胡伟..木薯AT-hook基序核定位基因家族的全基因组鉴定、表达谱及调控网络分析[J].热带作物学报,2025,46(10):2299-2313,15.基金项目
海南省自然科学基金联合项目(No.2021JJLH0034) （No.2021JJLH0034）
国家自然科学基金项目(No.32460528) （No.32460528）
"崖州湾"菁英人才科技专项项目(No.SCKJ-JYRC-2023-75). （No.SCKJ-JYRC-2023-75）
