Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans

Gongwei Chen,Xiulian Yang,Ling Li,Lianggui Wang,Yuli Li,Tingting Shi,Haiyan Li,Wenjie Ding,Yuanzheng Yue

doi:10.3390/f11020245

Gongwei Chen, Xiulian Yang + Show 7 more

Open Access

https://doi.org/10.3390/f11020245

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Journal: Forests	Publication Date: Feb 23, 2020
Citations: 10	License type: CC BY 4.0

Affiliation: Nanjing Forestry University, Cornell University

Abstract

Auxins have long been implicated in many aspects of plant growth and development. Auxin response factors (ARFs) are important proteins in auxin-mediated pathways and they play key roles in plant physiological and biochemical processes, including flower development. Endogenous indoleacetic acid (IAA) levels were measured and ARFs were studied in the flowers during the developmental stages in order to further elucidate the role of auxin in flower development of Osmanthus fragrans. A systematic analysis of OfARFs was conducted by carrying out a genome-wide search of ARFs. A total of 50 ARF genes (OfARFs) were detected and validated from the Osmanthus fragrans genome. Furthermore, a comprehensive overview of the OfARFs was undertaken, including phylogenetic relationship, gene structures, conserved domains, motifs, promoters, chromosome locations, gene duplications, and subcellular locations of the gene product. Finally, expression profiling, while using transcriptome sequencing from a previous study and quantitative real-time PCR (qRT-PCR), revealed that many OfARF genes have different expression levels in various tissues and flower developmental stages. By comparing the expression profiles among the flower developmental stages, and the relationship between ARFs and endogenous IAA levels, it can be supposed that OfARFs function in flower development of O. fragrans in an auxin-mediated pathway.

Highlights

Flowering is a crucial developmental stage in the life cycle of plants, especially for ornamental flowering plants [1]
Two strategies were employed to comprehensively identify the Auxin response factors (ARFs) in O. fragrans: BLASTP using the 23 full-length Arabidopsis ARF (AtARF) protein sequences previously identified as queries [34], and Hidden Markov Model (HMM) search with the AUX_RESP HMM model (PF06507) against the O. fragrans genome database
The entire collection of Osmanthus fragrans auxin response factor genes (OfARFs) that were identified in this study was named OfARF1 to OfARF29b, based on the homology relationship that was shown in the phylogenetic tree

Summary

Introduction

Flowering is a crucial developmental stage in the life cycle of plants, especially for ornamental flowering plants [1]. Previous studies have indicated that flowers react differently to the various endogenous phytohormone types and levels. A class of phytohormone previously reported to be an essential factor in plant growth and development, play a pivotal role in the development process of flowers, especially in floral primordium initiation and Forests 2020, 11, 245; doi:10.3390/f11020245 www.mdpi.com/journal/forests. Forests 2020, 11, 245 flower formation [3,4]. While considering the research basis of O. fragrans, exploring the auxin-mediated gene expression pathway, which is not studied in this species, should be beneficial for analyzing the function of auxin in regulating the flowering process

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