Bioinformatic Assessment and Expression Profiles of the AP2/ERF Superfamily in the Melastoma dodecandrum Genome

Abstract

AP2/ERF transcription factors play crucial roles in various biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, limited research has been conducted on the AP2/ERF genes of Melastoma dodecandrum for breeding of this potential fruit crop. Leveraging the recently published whole genome sequence, we conducted a comprehensive assessment of this superfamily and explored the expression patterns of AP2/ERF genes at a genome-wide level. A significant number of genes, totaling 218, were discovered to possess the AP2 domain sequence and displayed notable structural variations among five subfamilies. An uneven distribution of these genes was observed on 12 pseudochromosomes as the result of gene expansion facilitated by segmental duplications. Analysis of cis-acting elements within promoter sites and 87.6% miRNA splicing genes predicted their involvement in multiple hormone responses and abiotic stresses through transcriptional and post-transcriptional regulations. Transcriptome analysis combined with qRT-PCR results indicated that certain candidate genes are involved in tissue formation and the response to developmental changes induced by IAA hormones. Overall, our study provides valuable insights into the evolution of ERF genes in angiosperms and lays a solid foundation for future breeding investigations aimed at improving fruit quality and enhancing adaptation to barren land environments.

A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome

“…To investigate the expression patterns of the MedARF gene family, we obtained samples from three different organs of mature M. dodecandrum plants, namely leaves, stems, and roots. Additionally, hormone treatments were conducted on the naturally grown whole plants according to a method described by Zhou et al [28]. The treatments in this study included the application of exogenous auxin indole-3-acetic acid (IAA, 100 µM) and a growth hormone transport inhibitor, naphthylphthalamic acid (NPA, 100 µM) solution.…”

“…The relative gene expression levels were calculated using the 2 −∆∆Ct method based on the RT-qPCR data. The isolation of total RNA, reverse transcription, and RT-qPCR was performed according to a method described by Zhou et al [28]. The primer sequences for the target genes and the internal references can be found in the Supplementary Material (Table S5).…”

“…This progress has allowed us to gain valuable insights into the genetic makeup and organization of M. dodecandrum. Additionally, our research has led to the identification and analysis of several key gene functions [28,29], shedding light on the molecular mechanisms underlying important traits in M. dodecandrum. Building on our previous findings, the present study utilizes genomic data of M. dodecandrum to identify and analyze the structural characteristics and expression patterns of ARF genes.…”