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

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.

Flavonoids Accumulation in Fruit Peel and Expression Profiling of Related Genes in Purple (Passiflora edulis f. edulis) and Yellow (Passiflora edulis f. flavicarpa) Passion Fruits

“…The differential accumulation of flavonoid-related metabolites in both passion fruit cultivars was not only related to enzymatic activity but also structural gene expressions. According to previous studies, it was also related to some transcription factors such as MYB [57], BHLH [58], and WD40 [59], regulation of microRNA during protein expression and, ubiquitination and phosphorylation during protein activation [60].…”

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress

“…In addition, the Ka/Ks ratios were less than 1 in duplicated gene pairs from the K+ channel gene family in rice. This suggests that these genes have undergone purifying selection after duplication [61,62].…”

Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba

“…A total of 116 proteins contain the WD40 domain, and they are classified as subclass A. The 51 remaining GbWD40 genes consist of other domains, and they are categorized as subclasses B to P. In comparison with the classification of other plants, our results on the WD40 family genes in G. biloba show similarities and differences (Feng et al, 2019;Liu et al, 2020;Sun et al, 2020). The GbWD40 protein sequence is subjected to motif analysis.…”

“…They are highly conserved and abundant in eukaryotes, and they may play a key role in many biological processes, including signal transduction, protein trafficking, chromatin modification, and transcription (van Nocker et al, 2003;Stirnimann et al, 2010;Jain et al, 2018). The WD40 family is identified and analysed in many species (Hu et al, 2018;Salih et al, 2018;Feng et al, 2019;Liu et al, 2020). These results show that WD40 family genes are amplified to different extents in different plant evolutionary stages.…”