ArticleBMC genomics2015
Comprehensive analysis of CCCH-type zinc finger family genes facilitates functional gene discovery and reflects recent allopolyploidization event in tetraploid switchgrass.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Genome-wide identification of Hsf gene family in citrus and functional analysis of CsHsfA1a in heat stress response.Plant cell reports · 2026Article
- Genome-wide identification and immunological expression analysis of the C3HC4-type zinc finger protein genes in the silkworm, Bombyx Mori.BMC genomics · 2026Article
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- Comprehensive genome-wide characterization of NAC transcription factors in Barley influence insights into stress tolerance and evolutionary dynamics.Scientific reports · 2025Article
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- Comprehensive analysis of Metacrinus rotundus full length transcriptome.Scientific reports · 2025Article
- Genome-wide characterization of histone deacetylases inFrontiers in microbiology · 2025Article
- Genome-wide identification and expression analysis ofFrontiers in plant science · 2025Article
- "It's Only a Model": When Protein Structure Predictions Need Experimental Validation, the Case of the HTLV-1 Tax Protein.Pathogens (Basel, Switzerland) · 2024Review
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- Genome-Wide Identification and Evolution Analysis of theInternational journal of molecular sciences · 2023Article
- Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness.Scientific reports · 2023Article
- Genome-wide identification and characterization of the lettuce GASA family in response to abiotic stresses.BMC plant biology · 2023Article
- Zinc/iron-regulated transporter-like protein gene family inFrontiers in plant science · 2023Article
- STRONG STAYGREEN inhibits DNA binding of PvNAP transcription factors during leaf senescence in switchgrass.Plant physiology · 2022Article
- CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis.BMC plant biology · 2022Article
- Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family inFrontiers in plant science · 2022Article
- Genome-wide analysis and characterization of GRAS family in switchgrass.Bioengineered · 2021Article
- Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance.BMC plant biology · 2021Article
- CCCH protein-PvCCCH69 acted as a repressor for leaf senescence through suppressing ABA-signaling pathway.Horticulture research · 2021Article
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8 authors.
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Abstract
backgroundIn recent years, dozens of Arabidopsis and rice CCCH-type zinc finger genes have been functionally studied, many of which confer important traits, such as abiotic and biotic stress tolerance, delayed leaf senescence and improved plant architecture. Switchgrass (Panicum virgatum) is an important bioenergy crop. Identification of agronomically important genes and/or loci is an important step for switchgrass molecular breeding. Annotating switchgrass CCCH genes using translational genomics methods will help further the goal of understanding switchgrass genetics and creating improved varieties.
resultsTaking advantage of the publicly-available switchgrass genomic and transcriptomic databases, we carried out a comprehensive analysis of switchgrass CCCH genes (PvC3Hs). A total of 103 PvC3Hs were identified and divided into 21 clades according to phylogenetic analysis. Genes in the same clade shared similar gene structure and conserved motifs. Chromosomal location analysis showed that most of the duplicated PvC3H gene pairs are in homeologous chromosomes. Evolution analysis of 19 selected PvC3H pairs showed that 42.1% of them were under diversifying selection. Expression atlas of the 103 PvC3Hs in 21 different organs, tissues and developmental stages revealed genes with higher expression levels in lignified cells, vascular cells, or reproductive tissues/organs, suggesting the potential function of these genes in development. We also found that eight PvC3Hs in Clade-XIV were orthologous to ABA- or stress- responsive CCCH genes in Arabidopsis and rice with functions annotated. Promoter and qRT-PCR analyses of Clade-XIV PvC3Hs showed that these eight genes were all responsive to ABA and various stresses.
conclusionsGenome-wide analysis of PvC3Hs confirmed the recent allopolyploidization event of tetraploid switchgrass from two closely-related diploid progenitors. The short time window after the polyploidization event allowed the existence of a large number of PvC3H genes with a high positive selection pressure onto them. The homeologous pairs of PvC3Hs may contribute to the heterosis of switchgrass and its wide adaptation in different ecological niches. Phylogenetic and gene expression analyses provide informative clues for discovering PvC3H genes in some functional categories. Particularly, eight PvC3Hs in Clade-XIV were found involved in stress responses. This information provides a foundation for functional studies of these genes in the future.
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