ArticleBMC plant biology2022
Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses.
Article in BMC plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 24 citations in OpenAlex.
- Article
- Genome-Wide Identification and Expression Analysis of the PHD Finger Gene Family in Pea (Plants (Basel, Switzerland) · 2024Article
- Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae.BMC plant biology · 2023Article
- PHD finger proteins function in plant development and abiotic stress responses: an overview.Frontiers in plant science · 2023Review
- Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress inPlants (Basel, Switzerland) · 2022Article
- Two different domain architectures generate structural and functional diversity amongFrontiers in plant science · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies.
resultsWe performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper.
conclusionsOur data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.
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