Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum

Abstract

WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world’s citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.

Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress

“…The identified GRAS TFs were also renamed according to their chromosomal location by the nomenclature using GRAS + sequence number. Physicochemical properties were analyzed using ProtParam ( http://www.expasy.org/tools/protparam.html ) online software for molecular weight (MW), theoretical pI, amino acid number, and instability coefficient (aliphatic index) [ 78 ]. Subcellular localization was performed using the Plant-mPLoc (Plant-mPLoc server (sjtu.edu.cn)) online tool.…”

“…Gene Ontology function (GO) of the GRAS gene and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed on the GRAS genes of kiwifruit using TBtools. It was also mapped and visualized by the online tool ChiPlot ( https://www.chiplot.online/bar_plot_width_category ) [ 78 ].…”

Genome-wide identification and expression analysis of the MADS gene family in sweet orange (Citrus sinensis) infested with pathogenic bacteria

“…Next, 103 MADS gene sequences from Arabidopsis were downloaded from the TAIR database ( https://www.arabidopsis.org/ ). The BLASTP program was used to perform homology matching of the whole sweet orange genome using the MADS gene sequences of Arabidopsis as a reference ( Xi et al, 2023 ; Márquez Gutiérrez et al, 2022 ) to screen out the sequences of genes with an e-value >1e−5. Finally, the screening results were compared with the hmmsearch program to identify the MADS gene family members.…”