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

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

doi:10.7717/peerj.6628

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

PeerJ. 2019 Mar 26:7:e6628. doi: 10.7717/peerj.6628. eCollection 2019.

Authors

Xueqiang Su^#¹, Tiankai Meng^#², Yu Zhao¹, Guohui Li¹, Xi Cheng¹, Muhammad Abdullah¹, Xu Sun¹, Yongping Cai¹, Yi Lin¹

Affiliations

¹ School of Life Science, Anhui Agricultural University, Hefei, China.
² School of Life Sciences and Technology, TongJi University, Shanghai, China.

^# Contributed equally.

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.

Keywords: Chinese white pear; INDETERMINATE DOMAIN (IDD) genes; Lignin synthesis; Microsynteny; Phylogenetic analysis; SCW formation.

Grants and funding

This study was supported by the National Natural Science Foundation of China (Grant #31640068), the Anhui Provincial Natural Science Foundation (Grant #1808085QC79) and the Graduate innovation fund of Anhui Agricultural University (Grant #2018yjs-41). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.