ArticleBMC genomics2020
Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium).
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 59 citations in OpenAlex.
- Integrated phylogenomic and transcriptomic analyses reveal GhTZP3 as a key gene regulating flowering time and undergoing artificial selection in upland cotton (Gossypium hirsutum).Functional & integrative genomics · 2026Article
- Characterization of tomato AHL proteins and their biological functions in the resistance to salt and osmotic stresses.Plant cell reports · 2026Article
- Multi-genome comparative analysis and VIGS validation suggest thatFrontiers in plant science · 2026Article
- Analyses of gene families, allelic variation and VIGS reveal that GheIF3M.2 is significantly associated with dwarfism and the absence of flower buds in upland cotton.Functional & integrative genomics · 2025Article
- Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms inInternational journal of molecular sciences · 2025Article
- Genome-wide identification of boron transporters (GhBORs) in upland cotton and the role of GhBOR1 in promoting flowering.BMC plant biology · 2025Article
- Comprehensive evolutionary, differential expression and VIGS analyses reveal the function of GhNST1 in regulating drought tolerance and early maturity in upland cotton.Functional & integrative genomics · 2025Article
- Genome-Wide Analysis of the AT-Hook Gene Family inPlants (Basel, Switzerland) · 2025Article
- Genome-Wide Identification and Analysis of theInternational journal of molecular sciences · 2025Article
- Silencing ofFrontiers in plant science · 2025Article
- Genome of the most noxious weed water hyacinth (iScience · 2024Article
- Promoter of CassavaInternational journal of molecular sciences · 2024Article
- GhGASA14 regulates the flowering time of upland cotton in response to GAPlant cell reports · 2024Article
- Utilizing physiologies, transcriptomics, and metabolomics to unravel key genes and metabolites ofFrontiers in plant science · 2024Article
- Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses.PeerJ · 2024Article
- Genome-wide analysis of radishFrontiers in plant science · 2024Article
- Article
- Systematical Characterization of theInternational journal of molecular sciences · 2023Article
- AT-Hook Transcription Factors Show Functions inPlants (Basel, Switzerland) · 2023Article
- Transcriptome Analysis Reveals the Genes Related to Water-Melon Fruit Expansion under Low-Light Stress.Plants (Basel, Switzerland) · 2023Article
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10 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundMembers of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton.
resultsTo investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the specific WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules.
conclusionIn this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three types based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.
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