Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri).

Xueqiang Su,Xi Cheng,Tiankai Meng,Xu Sun,Guohui Li,Yu Zhao,Yongping Cai,Yi Lin,Muhammad Abdullah

doi:10.7717/peerj.6628

Abstract

The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.

Highlights

Zinc finger proteins are transcription factors with a finger-like domain that are widely distributed in animals, microorganisms, and the plant kingdom (Miller, Mclachlan & Klug, 1985)
Identification, characterization and phylogenetic analysis of INDETERMINATE DOMAIN (IDD) genes A total of 68 IDD proteins were identified and used for further analysis (Table 1; Table S1), which included 16 IDD proteins (PbIDD1-PbIDD16) in Chinese white pear
We identified a total of 52 IDD proteins in the other four species, including 14 in F. vesca (FvIDD1-FvIDD14), in Prunus mume (PmIDD1-PmIDD13), in R. occidentalis (RoIDD1-RoIDD14) and 11 in Prunus avium (PaIDD1-PaIDD11)

Summary

Introduction

Zinc finger proteins are transcription factors with a finger-like domain that are widely distributed in animals, microorganisms, and the plant kingdom (Miller, Mclachlan & Klug, 1985). Zinc finger proteins have been identified and functionally analysed in several plant species, such as Jatropha curcas (Shi et al, 2018), Oryza sativa (Zhang et al, 2018), Musa acuminata (Chen et al, 2014). One group of this large family of proteins, the INDETERMINATE DOMAIN (IDD) proteins, has a highly conserved ID domain (Colasanti, Yuan & Sundaresan, 1998), which contains typical C2H2 and C2HC zinc finger motifs (Wu et al, 2008). Zn2+ mainly plays a role in the linking of individual amino acid chains and is crucial to the function of zinc finger proteins (Islam, Hur & Wang, 2009; Tian et al, 2010)

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Conclusion