The WD40 Gene Family in Potato (Solanum Tuberosum L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s

Zhen Liu,Zhengpeng Cao,Baoyun Shen,Jeffrey A Coulter,Yuanming Li,Junlian Zhang,Chaozhou Li,Yuhui Liu

doi:10.3390/agronomy10030401

Abstract

WD40 proteins, also known as WD40 domain proteins, constitute a large gene family in eukaryotes and play multiple roles in cellular processes. However, systematic identification and analysis of WD40 proteins have not yet been reported in potato (Solanum tuberosum L.). In the present study, 178 potato WD40 (StWD40) genes were identified and their distribution on chromosomes, gene structure, and conserved motifs were assessed. According to their structural and phylogenetic protein features, these 178 StWD40 genes were classified into 14 clusters and 10 subfamilies. Collinearity analysis showed that segmental duplication events played a major role in the expansion of the StWD40 gene family. Synteny analysis indicated that 45 and 23 pairs of StWD40 genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively, and that these gene pairs evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-specific expression and abiotic stress-responsive StWD40 genes in doubled monoploid potato (DM). Furthermore, we further analyzed the WD40 genes might be involved in anthocyanin biosynthesis and drought stress in tetraploid potato cultivars based on RNA-seq data. In addition, a protein interaction network of two homologs of Arabidopsis TTG1, which is involved in anthocyanin biosynthesis, was constructed to identify proteins that might be related to anthocyanin biosynthesis. The result showed that there were 112 pairs of proteins interacting with TTG1, with 27 being differentially expressed in pigmented tissues. This study indicates that WD40 proteins in potato might be related to anthocyanin biosynthesis and abiotic stress responses.

Highlights

WD40 proteins, known as WD40 domain proteins, constitute a large gene family of eukaryotes [1]
The Hidden Markov Model (HMM) search was performed against the potato and Arabidopsis genomes, excluding sequences without a typical WD40 domain via the Pfam and SMART
A total of 178 StWD40 genes in potato and 232 AtWD40 genes in Arabidopsis were obtained, of which 230 AtWD40 genes were consistent with those identified by Li et al (2014) [31] and two more AtWD40 genes were identified in our work

Summary

Introduction

WD40 proteins, known as WD40 domain proteins, constitute a large gene family of eukaryotes [1]. Agronomy 2020, 10, 401 protein with a repeating 43 residue fragment containing highly a conserved glycine-histidine (GH) and tryptophan–aspartate (WD) motif [2]. The WD40 repeat proteins play multiple roles in cellular processes, including cell cycle regulation [6], cell apoptosis [7,8], autophagy [9,10], gene transcription [11], signal transduction [12,13], histone modification [14,15], DNA damage repair [16,17], RNA modification [18], cytoskeletal assembly, and chromatin assembly [19,20,21]. WD40 (TTG1) interacts with bHLH (basic-helix-loop-helix) and MYB (v-myb avian myeloblastosis viral oncogene homolog) to form the MBW (MYB-bHLH-WD40) complex, which regulates anthocyanin biosynthesis in Arabidopsis seedlings, and positively or negatively regulates the extension phase of fiber development [22]

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Conclusion