Cunyao Yan, Tao Yang, Baike Wang, Haitao Yang, Juan Wang, Qinghui Yu

Genes (Basel); 2023 Jun 15; 14(6):1273. doi: 10.3390/genes14061273.

Abstract

WD40 proteins are a superfamily of regulatory proteins widely found in eukaryotes that play an important role in regulating plant growth and development. However, the systematic identification and characterization of WD40 proteins in tomato (Solanum lycopersicum L.) have not been reported. In the present study, we identified 207 WD40 genes in the tomatoes genome and analyzed their chromosomal location, gene structure and evolutionary relationships. A total of 207 tomato WD40 genes were classified by structural domain and phylogenetic tree analyses into five clusters and 12 subfamilies and were found to be unevenly distributed across the 12 tomato chromosomes. We identified six tandem duplication gene pairs and 24 segmental duplication pairs in the WD40 gene family, with segmental duplication being the major mode of expansion in tomatoes. Ka/Ks analysis revealed that paralogs and orthologs of WD40 family genes underwent mainly purifying selection during the evolutionary process. RNA-seq data from different tissues and developmental periods of tomato fruit development showed tissue-specific expression of WD40 genes. In addition, we constructed four coexpression networks according to the transcriptome and metabolome data for WD40 proteins involved in fruit development that may be related to total soluble solid formation. The results provide a comprehensive overview of the tomato WD40 gene family and will provide valuable information for the validation of the function of tomato WD40 genes in fruit development.

See https://pubmed.ncbi.nlm.nih.gov/37372453/

Figure 1. Chromosomal distribution of WD40 family genes in tomato. (A) Distribution of tomato WD40 genes on 12 chromosomes. Tandemly duplicated genes are marked with colored boxes. (B) Number of tomato WD40 genes on each chromosome. Blue lines in chromosome segments represent low gene density and red lines represent high gene density.