Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress

Abstract

Background Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions. Results In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus. Conclusions This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree’s response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.

Glutathione Promotes Degradation and Metabolism of Residual Fungicides by Inducing UDP-Glycosyltransferase Genes in Tomato

“…Transcription factors (TFs) are important proteins, which bind to specific DNA motifs, regulate gene expression and play an important role in plant stress response ( Wu et al, 2022 ). The present study found that 121 tomato UGT genes interacted with 12 different transcription factors, 90% of which were regulated by glutathione under CHT stress.…”

Identification and characteristics of SnRK genes and cold stress-induced expression profiles in Liriodendron chinense

“…RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). The library preparations were sequenced on an Illumina Novaseq 6000 platform, and 150 bp paired-end reads were generated [ 89 ]. Three replicates were set for each independent experiment.…”

Identification, Phylogenetic and Expression Analyses of the AAAP Gene Family in Liriodendron chinense Reveal Their Putative Functions in Response to Organ and Multiple Abiotic Stresses

“…According to previous studies, AAAPs were involved in the low temperature, heat temperature, drought stress treatments in many plants [35,54,55]. In this study, we analyze the LcAAAP gene expression pattern based on the stress transcriptome data of hybrid Liriodendron [56,57]. A total of 13 genes in hybrid Liriodendron leaves were able to respond to the three abiotic stress treatments.…”

“…How plants adapt to external abiotic stresses involves a very complex gene regulatory network, and a variety of transcription factors are usually involved in this process [58][59][60]. In previous studies, we found that WRKY and MYB genes were involved in regulating the response of hybrid Liriodendron to stress [56,57]. Therefore, we constructed the co-expression network based on the LcAAAP, LcMYB, and LcWRKY genes to explore the interactions between them.…”

“…Therefore, we constructed the co-expression network based on the LcAAAP, LcMYB, and LcWRKY genes to explore the interactions between them. Multiple MYB and WRKY genes showed a significantly positive correlation, and LcWRKY5/27 and LcMYB9/28/83 could rise to a relatively high level in a short time under abiotic stress [56,57]. These results indicated that the LcLHT1, LcAPP4a, and LcATL5a could transport amino acids under abiotic stress, provide support for the internal homeostasis of plants, and then adapt to changes in the external environment, and the specific expression pattern of these genes was directly or indirectly regulated by upstream transcription factors.…”