Genome-Wide Identification of the WD40 Gene Family in Tomato (Solanum lycopersicum L.).

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.

Genome-wide identification and expression pattern analysis of lipoxygenase gene family in turnip (Brassica rapa L. subsp. rapa).

Turnip (Brassica rapa L. subsp. rapa) is an important crop with edible and medicinal values, and various stresses, especially salt stress and drought stress, seriously threaten the yield of turnips. LOXs play important roles in regulating plant growth and development, signal transduction, and biotic and abiotic stress responses through secondary metabolites produced by the oxylipin metabolic pathway, and although the turnip genome has been published, however, the role of LOX family genes in various abiotic stress responses has not been systematically studied in turnips. In this study, a total of 15 LOX genes (BrrLOX) were identified in turnip, distributed on six chromosomes. Phylogenetic tree analysis classified these LOX genes into two classes: three 9-LOX proteins and 12 13-LOX type II proteins. Gene duplication analysis showed that tandem and segmental duplication were the main pathways for the expansion of the BrrLOX gene family. The Ka and Ks values of the duplicated genes indicate that the BrrLOX gene underwent strong purifying selection. Further analysis of the cis-acting elements of the promoters suggested that the expression of the BrrLOX gene may be influenced by stress and phytohormones. Transcriptome data analysis showed that 13 BrrLOX genes were expressed at one or more stages of turnip tuber development, suggesting that LOX genes may be involved in the formation of turnip fleshy roots. The qRT-PCR analysis showed that four stresses (salt stress, drought stress, cold stress, and heat stress) and three hormone treatments (methyl jasmonate, salicylic acid, and abscisic acid) affected the expression levels of BrrLOX genes and that different BrrLOX genes responded differently to these stresses. In addition, weighted gene co-expression network analysis (WGCNA) of BrrLOX revealed seven co-expression modules, and the genes in these co-expression modules are collectively involved in plant growth and development and stress response processes. Thus, our results provide valuable information for the functional identification and regulatory mechanisms of BrrLOX in turnip growth and development and stress response.

Genome-wide identification and expression analysis of the JAZ gene family in turnip.

JAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.