AUTHOR=Su Shenghui , Ji Min , Chen Jiaqi , Zhang Meidie , Xu Xiaozhao , Cheng Chenxia 

TITLE=Genome-wide identification and expression analysis of protein arginine methyltransferase and JmjC domain-containing family in apple

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1381753

DOI=10.3389/fpls.2024.1381753

ISSN=1664-462X

ABSTRACT=<p>Histone methylation is an important type of histone modification that regulates gene expression in plants. In this study, we identified 14 arginine methylation-related genes (<italic>Protein Arginine Methyltransferase</italic>, <italic>MdPRMT</italic>) and 32 demethylation-related genes (<italic>JmjC Domain-Containing Family</italic>, <italic>MdJMJ</italic>) in apple. Furthermore, we investigated the phylogenetic relationship, chromosome distribution, gene structure, motif analysis, promoter sequence analysis, and expression patterns of <italic>MdPRMT</italic> and <italic>MdJMJ</italic> genes. Homology analysis showed a high degree of conservation and homology between <italic>PRMT</italic> and <italic>JMJ</italic> genes in <italic>Arabidopsis</italic> and apple. We identified the types of duplicated genes in the <italic>MdJMJ</italic> and <italic>MdPRMT</italic> gene families, found a large number of whole-genome duplicates (WGD) gene pairs and a small number of tandem duplicates (TD) pairs, transposed duplication (TRD) gene pairs as well as proximal duplicates (PD) pairs, and discussed the possible evolutionary pathways of the gene families from the perspective of duplicated genes. Homology analysis showed a high degree of conservation and homology between <italic>PRMT</italic> and <italic>JMJ</italic> genes in <italic>Arabidopsis</italic> and apple. In addition, the promoter regions of <italic>MdPRMT</italic> and <italic>MdJMJ</italic> contain numerous <italic>cis</italic>-acting elements involved in plant growth and development, hormone response, and stress responses. Based on the transcriptional profiles of <italic>MdPRMT</italic> and <italic>MdJMJ</italic> in different tissues and developmental stages, it was found that <italic>MdPRMT</italic> and <italic>MdJMJ</italic> may play multiple roles in apple growth and development, for example, <italic>MdJMJ21</italic> may be involved in the regulation of apple endosperm formation. <italic>MdPRMT</italic> and <italic>MdJMJ</italic> exhibit different expression patterns in response to hormone signaling in apple, <italic>MdJMJ3</italic>, <italic>MdJMJ18</italic>, <italic>MdJMJ30</italic>, <italic>MdPRMT2</italic>, <italic>MdPRMT13</italic>, and <italic>MdPRMT14</italic> may play roles in apple response to drought stress, while the expression of <italic>MdJMJ13</italic>, <italic>MdPRMT3</italic>, <italic>MdPRMT4</italic>, and <italic>MdPRMT6</italic> is affected by cold stress. Our study provides a foundation for determining the functional roles of <italic>MdPRMT</italic> and <italic>MdJMJ</italic> genes in apple.</p>