Abstract
BackgroundAPETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformation and flower organ development in many plants. However, the roles of miR172 and its target AP2 genes remain largely unknown in Brassica napus (B. napus).ResultsIn this study, 19 euAP2 and four miR172 genes were identified in the B. napus genome. A sequence analysis suggested that 17 euAP2 genes were targeted by Bna-miR172 in the 3′ coding region. EuAP2s were classified into five major groups in B.napus. This classification was consistent with the exon-intron structure and motif organization. An analysis of the nonsynonymous and synonymous substitution rates revealed that the euAP2 genes had gone through purifying selection. Whole genome duplication (WGD) or segmental duplication events played a major role in the expansion of the euAP2 gene family. A cis-regulatory element (CRE) analysis suggested that the euAP2s were involved in the response to light, hormones, stress, and developmental processes including circadian control, endosperm and meristem expression. Expression analysis of the miR172-targeted euAP2s in nine different tissues showed diverse spatiotemporal expression patterns. Most euAP2 genes were highly expressed in the floral organs, suggesting their specific functions in flower development. BnaAP2–1, BnaAP2–5 and BnaTOE1–2 had higher expression levels in late-flowering material than early-flowering material based on RNA-seq and qRT-PCR, indicating that they may act as floral suppressors.ConclusionsOverall, analyses of the evolution, structure, tissue specificity and expression of the euAP2 genes were peformed in B.napus. Based on the RNA-seq and experimental data, euAP2 may be involved in flower development. Three euAP2 genes (BnaAP2–1, BnaAP2–5 and BnaTOE1–2) might be regarded as floral suppressors. The results of this study provide insights for further functional characterization of the miR172 /euAP2 module in B.napus.
Highlights
APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 binding site
Identification of euAP2 and miR172 genes in B. napus Eight characterized AP2 protein sequences in Arabidopsis were used as the query sequences to identify the euAP2 gene family in the B. napus genome using BLASTP searches with an E-value of ≤10− 10, and 19 putative euAP2 family genes were identified
The predicted molecular weight (Mw) of these deduced proteins varied from 11.00 kDa to
Summary
APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformation and flower organ development in many plants. MicroRNAs are a class of endogenous, small non-coding RNAs (20–24 nucleotides) with critical roles in the posttranscriptional regulation of gene expression [1]. Plant miRNAs have been reported to be involved in many biological processes, such as auxin signalling [2], flowering time regulation [3], leaf development [4] and stress responses [5, 6]. The miR172 family is a major component of the age pathway, and it is encoded by MIR172a-e genes in Arabidopsis. The AP2 proteins have one or more AP2 domains consisting of 60–70 highly conserved amino acids (aa) and two conserved components, namely, the YRG and RAYDmotifs, at the N- and C-terminus of the AP2 domain respectively [23,24,25]
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