Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses

Background The 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. Results We 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. Conclusions Our 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.

Automated summary

In this study, we performed genome-wide re-annotation of PHD-finger genes in Arabidopsis thaliana, Oryza sativa, Capsicum annuum, Solanum tuberosum, and Solanum lycopersicum. We identified new PHD-finger genes and revealed the diversification of their structures and functions. Evolutionary analysis showed lineage-specific duplication of PHD-finger genes, particularly in pepper and potato. Expression validation and transcriptome analysis in pepper suggested potential functions of PHD-finger genes in response to abiotic stresses.