HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume

Abstract

Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight Rosaceae plants of which 13 PmHDACs genes are from P. mume. A phylogenetic analysis suggests that the RoHDACs family is classified into three subfamilies, HDA1/RPD3, HD2, and SIR2. We identify 11 segmental duplication gene pairs of RoHDACs and find, via a sequence alignment, that the HDACs gene family, especially the plant-specific HD2 family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three HDACs subfamilies has its own conserved domains. The expression of PmHDACs in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all PmHDACs genes—especially PmHDA1/6/14, PmHDT1, and PmSRT1/2—significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the HDACs family in Rosaceae plants. Expression profiles of PmHDACs in response to cold stress could provide an important clue to improve the cold hardiness of mei.

Histone deacetylase 9 regulates disease resistance through fine‐tuning histone deacetylation of melatonin biosynthetic genes and melatonin accumulation in cassava

“…HDAs play vital roles in the negative regulation of transcriptional expression during different developmental processes and environmental stress signaling in plants. [42][43][44][45][46][47] Due to the transcriptional reprogramming by HDAs, the involvement of HDAs in plant stress responses has been widely reported in model plants (Arabidopsis, rice, etc.). [45][46][47][48][49][50] Here, this study not only identifies MeHDA9 as a novel regulator of cassava disease resistance, but also illustrates the direct relationship between MeHDA9-mediated histone deacetylation and melatonin biosynthesis in immune responses.…”

“…HDAs play vital roles in the negative regulation of transcriptional expression during different developmental processes and environmental stress signaling in plants 42–47 . Due to the transcriptional reprogramming by HDAs, the involvement of HDAs in plant stress responses has been widely reported in model plants (Arabidopsis, rice, etc.)…”

Comparative Genomics and Functional Genomics Analysis in Plants

“…Another abiotic stress capable of significantly impacting plants is low temperature. The comparative genome and RNA-seq data analysis of eight rosaceae genomes revealed the significant response of PmHDACs genes to cold stress in Prunus mume [ 2 ]. Liu et al (2022) [ 3 ] applied a controlled atmosphere (CA) treatment to peach fruit and explored its effects on alleviating a chilling injury and maintaining the fruit flavor quality.…”