Genome-wide identification and characterization of auxin response factor (ARF) family genes related to flower and fruit development in papaya (Carica papaya L.).

Kaidong Liu,Haili Li,Xiaolin Zheng,Wanhuang Lin,Changchun Yuan,Yanjun Yang,Chenjia Shen

doi:10.1186/s12864-015-2182-0

Abstract

BackgroundAuxin and auxin signaling are involved in a series of developmental processes in plants. Auxin Response Factors (ARFs) is reported to modulate the expression of target genes by binding to auxin response elements (AuxREs) and influence the transcriptional activation of down-stream target genes. However, how ARF genes function in flower development and fruit ripening of papaya (Carica papaya L.) is largely unknown. In this study, a comprehensive characterization and expression profiling analysis of 11 C. papaya ARF (CpARF) genes was performed using the newly updated papaya reference genome data.ResultsWe analyzed CpARF expression patterns at different developmental stages. CpARF1, CpARF2, CpARF4, CpARF5, and CpARF10 showed the highest expression at the initial stage of flower development, but decreased during the following developmental stages. CpARF6 expression increased during the developmental process and reached its peak level at the final stage of flower development. The expression of CpARF1 increased significantly during the fruit ripening stages. Many AuxREs were included in the promoters of two ethylene signaling genes (CpETR1 and CpETR2) and three ethylene-synthesis-related genes (CpACS1, CpACS2, and CpACO1), suggesting that CpARFs might be involved in fruit ripening via the regulation of ethylene signaling.ConclusionsOur study provided comprehensive information on ARF family in papaya, including gene structures, chromosome locations, phylogenetic relationships, and expression patterns. The involvement of CpARF gene expression changes in flower and fruit development allowed us to understand the role of ARF-mediated auxin signaling in the maturation of reproductive organs in papaya.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2182-0) contains supplementary material, which is available to authorized users.

Highlights

Auxin and auxin signaling are involved in a series of developmental processes in plants
It has been shown that auxin coordinates plant development essentially through the transcriptional regulation of some gene families, such as auxin/indole-3-acetic acid (Aux/Indole-3-acetic acid (IAA)), Gretchen Hagen3 (GH3), small auxin up RNA (SAUR), and auxin response factor (ARF) [4, 5]
These genes were named according to the phylogenetic relationships between C. papaya and Arabidopsis

Summary

Introduction

Auxin and auxin signaling are involved in a series of developmental processes in plants. Auxin Response Factors (ARFs) is reported to modulate the expression of target genes by binding to auxin response elements (AuxREs) and influence the transcriptional activation of down-stream target genes. It has been shown that auxin coordinates plant development essentially through the transcriptional regulation of some gene families, such as auxin/indole-3-acetic acid (Aux/IAA), Gretchen Hagen (GH3), small auxin up RNA (SAUR), and auxin response factor (ARF) [4, 5]. Being an important component of auxin signaling pathway, ARFs activate or repress the expression of auxin response genes by binding to AuxRE in their promoter [8]. A typical ARF contains a highly conserved N-terminal B3-like DNA binding domain (DBD) that recognizes AuxRE in the promoter of auxin-responsive genes [8]. The middle region (MR), located between DBD and CTD, confers transcriptional activation or repression depending on its amino acid composition [8, 11]

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Conclusion