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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 various 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 features 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 mechanism 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 domains and motifs showed that all MeAHLs had the PPC/DUF296 domain and AT-hook motif. Members of Clade A generally 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. Protein-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 systematic characterization of AHL family evolution and functional diversification in cassava, offering theoretical foundations for molecular breeding applications.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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