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.

Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

In plantae, basic leucine zipper (bZIP) transcription factors (TFs) are widespread and regulate a variety of biological processes under abiotic stress. However, it has not been extensively studied in Rosaceae, and the functional effects of bZIP on Eriobotrya japonica under salt stress are still unknown. Therefore, in this study, the bZIP TF family of 12 species of Rosaceae was analyzed by bioinformatics method, and the expression profile and quantitative real‐time polymerase chain reaction of E. japonica under salt stress were analyzed. The results showed that a total of 869 bZIP TFs were identified in 12 species of Rosaceae and divided into nine subfamilies. Differences in promoter cis‐elements between subfamilies vary depending on their role. Species belonging to the same subfamily have a similar number of chromosomes and the number of genes contained on each chromosome. Gene duplication analysis has found segmental duplication to be a prime force in the evolution of Rosaceae species. In addition, nine EjbZIPs were significantly different, including seven up‐regulated and two down‐regulated in E. japonica under salt stress. Especially, EjbZIP13 was involved in the expression of SA‐responsive proteins by binding to the NPR1 gene. EjbZIP27 , EjbZIP30 , and EjbZIP38 were highly expressed in E. japonica under salt stress, thus improving the salt tolerance capacity of the plants. These results can provide a theoretical basis for exploring the characteristics and functions of the bZIP TF family in more species and breeding salt‐tolerant E. japonica varieties. It also provides a reference for resolving the response mechanism of bZIP TF in 12 Rosaceae species under salt stress.

(1) Background: The sweet orange (Citrus sinensis) is the most widely cultivated and productive citrus fruit in the world, with considerable economic value and good prospects for development. However, post-harvest storage and transport of the fruit are often affected by infestation by Penicillium species, leading to many losses. (2) Methods: In this study, the family of bZIP genes from the whole genome of sweet orange was identified and analyzed in detail in terms of gene structure, physicochemical properties, protein structure, conserved structural domains, chromosomal positioning, and promoter analysis using bioinformatic analysis, in addition to an analysis of the expression patterns of the fruit following Penicillium infection. (3) Results: In this study, 50 CsbZIP genes were identified from the sweet orange genome. In silico analysis showed that Cs_ont_3g005140 was presumably localized in the chloroplasts, while the rest of the family members were located in the nucleus. Phylogenetic trees of grape, apple, Arabidopsis, and sweet orange were constructed on the basis of evolutionary relationships and divided into 16 subfamilies. Conserved motif analysis showed that all CsbZIP family genes encode proteins containing the highly conserved Motif 1. Promoter prediction analysis showed the chromosomal positioning, and the covariance analysis showed that the 50 CsbZIPs were unevenly distributed on nine chromosomes, with 10 pairs of duplicated genes. In the analysis of expression patterns, 11 of the 50 CsbZIP genes were not expressed, 12 were upregulated, 27 were downregulated, and five of the upregulated genes were highly expressed. (4) Conclusions: In this study, two CsbZIP members were each closely related to two Arabidopsis thaliana genes associated with salt stress. The functions of the replicated and re-differentiated CsbZIP homologs (Cs_ont_1g027160 and Cs_ont_8g020880) divergee further, with one responding to inoculation by Penicillium and the other not doing so. Five genes associated with sweet orange in response to Penicillium infestation were initially screened (Cs_ont_3g000400, Cs_ont_3g003210, Cs_ont_5g007090, Cs_ont_5g011180, Cs_ont_8g020880). This study provides some theoretical basis for subsequent research into the response mechanism of sweet orange bZIP transcription factors under biotic stresses.

Saccharomyces uvarum is one of the few fermentative species that can be used in winemaking, but its weak sulfite tolerance is the main reason for its further use. Previous studies have shown that the expression of the methionine synthase gene (MET4) is upregulated in FZF1 (a gene encoding a putative zinc finger protein, which is a positive regulator of the transcription of the cytosolic sulfotransferase gene SSU1) overexpression transformant strains, but its exact function is unknown. To gain insight into the function of the MET4 gene, in this study, a MET4 overexpression vector was constructed and transformed into S. uvarum strain A9. The MET4 transformants showed a 20 mM increase in sulfite tolerance compared to the starting strain. Ninety-two differential genes were found in the transcriptome of A9-MET4 compared to the A9 strain, of which 90 were upregulated, and two were downregulated. The results of RT-qPCR analyses confirmed that the expression of the HOMoserine requiring gene (HOM3) in the sulfate assimilation pathway and some fermentation-stress-related genes were upregulated in the transformants. The overexpression of the MET4 gene resulted in a significant increase in sulfite tolerance, the upregulation of fermentation-stress-related gene expression, and significant changes in the transcriptome profile of the S. uvarum strain.