ArticlePloS one2012
Genome-wide identification, evolutionary expansion, and expression profile of homeodomain-leucine zipper gene family in poplar (Populus trichocarpa).
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 111 citations in OpenAlex.
- Genome-wide analysis of class III peroxidase gene family in Glycine max and functional roles in stress response.Scientific reports · 2025Article
- Genome-wide identification and expression analysis of HD-ZIP gene family in sunflower (Helianthus annuus L.) under water deficit stress.Scientific reports · 2025Article
- The ASYMMETRIC LEAVES1 ortholog PagAS1a promotes xylem development and plant growth inForestry research · 2025Article
- Genome-wide characterisation of HD-Zip transcription factors and functional analysis of PbHB24 during stone cell formation in Chinese white pear (Pyrus bretschneideri).BMC plant biology · 2024Article
- Genome-Wide Identification, Characterization, and Expression Analysis of the HD-Zip Gene Family inGenes · 2024Article
- Comprehensive bioinformation analysis of homeodomain-leucine zipper gene family and expression pattern of HD-Zip I under abiotic stress in Salix suchowensis.BMC genomics · 2024Article
- Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants.Journal of molecular evolution · 2023Review
- Genome-Wide Identification of Homeodomain Leucine Zipper (HD-ZIP) Transcription Factor, Expression Analysis, and Protein Interaction of HD-ZIP IV in Oil Palm Somatic Embryogenesis.International journal of molecular sciences · 2023Article
- Genome-wide identification, bioinformatics and expression analysis of HD-Zip gene family in peach.BMC plant biology · 2023Article
- Genome-wide identification of HD-ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum.The plant genome · 2023Article
- Article
- Genome-wide identification and characterization of the HD-Zip gene family and expression analysis in response to stress inPlant signaling & behavior · 2022Article
- Genome-Wide Characterization and Expression Profiling of HD-Zip Genes in ABA-Mediated Processes inPlants (Basel, Switzerland) · 2022Article
- Article
- Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in SugarcaneInternational journal of molecular sciences · 2022Article
- Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage.Molecular biology reports · 2022Article
- Genome-Wide Characterization and Expression Analysis of HD-ZIP Gene Family inFrontiers in genetics · 2022Article
- A moso bamboo transcription factor, Phehdz1, positively regulates the drought stress response of transgenic rice.Plant cell reports · 2021Article
- Genome-Wide Characterization and Expression Analysis of the HD-ZIP Gene Family in Response to Salt Stress in Pepper.International journal of genomics · 2021Article
- Four HD-ZIPs are involved in banana fruit ripening by activating the transcription of ethylene biosynthetic and cell wall-modifying genes.Plant cell reports · 2020Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHomeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. PRINCIPAL
findingsIn this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I-IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns.
conclusionsGenomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles.
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