Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensisSonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission

Yanqing Zhang,Caiqin Li,Chengjie Chen,Jianguo Li,Zaohai Zeng,Rui Xia

doi:10.7717/peerj.6677

Abstract

Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.

Highlights

Auxin plays a central role in numerous aspects of plant developmental and physiological processes, including embryogenesis, apical dominance, vascular elongation, flowering, fruit development, and lateral root initiation (Woodward & Bartel, 2005; Fleming, 2006)
Identification and phylogenetic analysis of LcARF genes To identify all Auxin response factors (ARFs) members in litchi, protein sequences of ARFs in rice, Arabidopsis and tomato were used as queries in BLASTP to search against a litchi annotated gene database
In our RNA-seq survey of ARF gene expression, we found that most of the ARF genes show an opposite correlation with the fruit abscission, that is, ARF genes were down-regulated by abscission induced treatments (ETH and girdling plus defoliation (GPD)), but up-regulated by GPDD, in which the abscission of GPD was inhibited by the addition of 2, 4-D

Summary

Introduction

Auxin plays a central role in numerous aspects of plant developmental and physiological processes, including embryogenesis, apical dominance, vascular elongation, flowering, fruit development, and lateral root initiation (Woodward & Bartel, 2005; Fleming, 2006). Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission. A typical ARF is characterized by a highly conserved N-terminal B3-type DNA binding domain (DBD) that recognized the AuxRE motif, an activation domain or repression domain, and a carboxy-terminal dimerization domain (domain III/IV), which is involved in protein–protein interactions by dimerizing with auxin/indole-3-acetic acid (Aux/IAA) family genes (Kim, Harter & Theologis, 1997; Guilfoyle & Hagen, 2007; Piya et al, 2014). AtARF9 acts in suspensor cells to mediate hypophysis specification (Rademacher et al, 2012), and AtARF10/16/17 play vital roles in negatively regulating seed germination and post-germination activities (Liu et al, 2007)

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