Lipoxygenases (LOXs) are non-heme iron-containing dioxygenases involved in many developmental and stress-responsive processes in plants. However, little is known about the radish LOX gene family members and their functions in response to biotic and abiotic stresses. In this study, we completed a genome-wide analysis and expression profiling of RsLOX genes under abiotic and biotic stress conditions. We identified 11 RsLOX genes, which encoded conserved domains, and classified them in 9-LOX and 13-LOX categories according to their phylogenetic relationships. The characteristic structural features of 9-LOX and 13-LOX genes and the encoded protein domains as well as their evolution are presented herein. A qRT-PCR analysis of RsLOX expression levels in the roots under simulated drought, salinity, heat, and cold stresses, as well as in response to a Plasmodiophora brassicae infection, revealed three tandem-clustered RsLOX genes that are involved in responses to various environmental stresses via the jasmonic acid pathway. Our findings provide insights into the evolution and potential biological roles of RsLOXs related to the adaptation of radish to stress conditions.

Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach. We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways. Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives.

Plant heat shock factors (Hsfs) play crucial roles in various environmental stress responses. Eggplant (Solanum melongena L.) is an agronomically important and thermophilic vegetable grown worldwide. Although the functions of Hsfs under environmental stress conditions have been characterized in the model plant Arabidopsis thaliana and tomato, their roles in responding to various stresses remain unclear in eggplant. Therefore, we characterized the eggplant SmeHsf family and surveyed expression profiles mediated by the SmeHsfs under various stress conditions. Here, using reported Hsfs from other species as queries to search SmeHsfs in the eggplant genome and confirming the typical conserved domains, we identified 20 SmeHsf genes. The SmeHsfs were further classified into 14 subgroups on the basis of their structure. Additionally, quantitative real-time PCR revealed that SmeHsfs responded to four stresses—cold, heat, salinity and drought—which indicated that SmeHsfs play crucial roles in improving tolerance to various abiotic stresses. The expression pattern of SmeHsfA6b exhibited the most immediate response to the various environmental stresses, except drought. The genome-wide identification and abiotic stress-responsive expression pattern analysis provide clues for further analysis of the roles and regulatory mechanism of SmeHsfs under environmental stresses.

Pak choi is one of the most important leafy vegetables planted in East Asia and provides essential nutrients for the human body. Purple pak choi differs mainly in leaf colour but exhibits distinct nutritional profiles from green pak choi. In this study, we performed metabolic and transcriptomic analyses to uncover the mechanisms underlying the differences in metabolite biosynthesis profiles between the two pak choi varieties. Metabolite profiling revealed significant differences in the levels of metabolites, mainly amino acids and their derivatives and flavonoids. Furthermore, 34 flavonoids significantly differed between green and purple pak choi leaves, and cyanidin and its derivative anthocyanins were abundant in purple pak choi. In addition, we found that the structural genes CHS, DFR, ANS, and UGT75C1, as well as the transcription factor MYB2, play a major role in anthocyanin synthesis. These results provide insight into the molecular mechanisms underlying leaf pigmentation in pak choi and offer a platform for assessing related varieties.

Background: Sugar not only is an important biomacromolecule that plays important roles in plant growth, development, and biotic and abiotic stress tolerance but also provides a skeleton for other macromolecules, such as proteins and nucleic acids. Sugar transporter proteins (STPs) play essential roles in plant sugar transport and ultimately affect the abovementioned life processes. However, the evolutionary dynamics of this important gene family in Brassicaceae crops are still largely unknown, and the functional differentiation of radish STP genes remains unclear. Results: In the present study, a comparative genomic study of STP genes in five representative Brassicaceae crops was conducted, and a total of 25, 25, 28, 36 and 49 STP genes were individually identified in Raphanus sativus (Rs), Brassica oleracea (Bo), B. rapa (Br), B. napus (Bn) and B. juncea (Bj), which were divided into four clades by phylogenetic analysis. The number of STP genes was no direct correlation with genome size and the total number of coding genes in Brassicaceae crops, and their physical and chemical properties showed no significant difference. Expression analysis showed that radish STP genes play vital roles not only in flower and seedpod development but also under heavy metal (cadmium, chromium and lead), NaCl and PEG-6000 stresses, Agrobacterium tumefaciens infection, and exogenous sugar treatment. RsSTP13.2 was significantly upregulated in the resistant radish cultivar by A. tumefaciens infection and induced by heavy metal, NaCl and PEG-6000 stress, indicating that it is involved in resistance to both biotic and abiotic stress in radish. Conclusions: The present study provides insights into the evolutionary patterns of the STP gene family in Brassicaceae genomes and provides a theoretical basis for future functional analysis of STP genes in Brassicaceae crops.