Genome-wide analysis of the Tritipyrum WRKY gene family and the response of TtWRKY256 in salt-tolerance

IntroductionThe transcription factor WRKY is widespread in the plant kingdom and plays a crucial role in diverse abiotic stress responses in plant species. Tritipyrum, an octoploid derived from an intergeneric cross between Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), is a valuable germplasm resource for introducing superior traits of Th. elongatum into T. aestivum. The recent release of the complete genome sequences of T. aestivum and Th. elongatum enabled us to investigate the organization and expression profiling of Tritipyrum WRKY genes across the entire genome.ResultsIn this study, 346 WRKY genes, from TtWRKY1 to TtWRKY346, were identified in Tritipyrum. The phylogenetic analysis grouped these genes into three subfamilies (I-III), and members of the same subfamilies shared a conserved motif composition. The 346 TtWRKY genes were dispersed unevenly across 28 chromosomes, with 218 duplicates. Analysis of synteny suggests that the WRKY gene family may have a common ancestor. Expression profiles derived from transcriptome data and qPCR demonstrated that 54 TtWRKY genes exhibited relatively high levels of expression across various salt stresses and recovery treatments. Tel1E01T143800 (TtWRKY256) is extremely sensitive to salt stress and is on the same evolutionary branch as the salt-tolerant A. thaliana genes AtWRKY25 and AtWRKY33. From 'Y1805', the novel AtWRKY25 was cloned. The Pearson correlation analysis identified 181 genes that were positively correlated (R>0.9) with the expression of TtWRKY256, and these genes were mainly enriched in metabolic processes, cellular processes, response to stimulus, biological regulation, and regulation of biological. Subcellular localization and qRT-PCR analysis revealed that TtWRKY256 was located in the nucleus and was highly expressed in roots, stems, and leaves under salt stress.DiscussionThe above results suggest that TtWRKY256 may be associated with salt stress tolerance in plants and may be a valuable alien gene for improving salt tolerance in wheat

Comparing the Transcriptomes of Two Different Tissues in Helicoverpa assulta (Guenée)

Helicoverpa assulta (Guenée), a moth species belonging to the Noctuidae (Lepidoptera) family, is a destructive agricultural pest that infests multiple cash crops. To assess differences in the gene expression profiles of different tissues in H. assulta, we analyzed the transcriptomes of two tissue types (midgut and hemocytes) using the Illumina Hiseq 2000 platform, on the basis of which we obtained 52076750 and 53404200 high-quality clean reads, respectively. De novo assembly yielded 46146 and 33707 unigenes from the midgut and hemocytes, respectively. After screening, we identified 23726 unigenes differentially expressed between the midgut and hemocytes. Taking the midgut as the control, we detected 7448 and 16278 unigenes that were up- and downregulated in hemocytes, respectively. Gene Ontology functional annotation divided the differentially expressed unigenes (DEUs) into three categories (biological process, cellular component, and molecular function) and 51 branches, whereas the Kyoto Encyclopedia of Genes and Genomes metabolic pathway annotation assigned the DEUs to six categories, mapping these to 258 pathways. In addition, we detected 224918 single-nucleotide polymorphic sites. Our findings based on transcriptome sequencing, data assembly, and functional gene annotation of two different tissues in H. assulta will provide a valuable reference for further excavation and study of functional genes in H. assulta.</jats:p

Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L.

Abstract Background The basic leucine zipper (bZIP) transcription factor (TF) is one of the largest families of transcription factors (TFs). It is widely distributed and highly conserved in animals, plants, and microorganisms. Previous studies have shown that the bZIP TF family is involved in plant growth, development, and stress responses. The bZIP family has been studied in many plants; however, there is little research on the bZIP gene family in tobacco. Results In this study, 77 bZIPs were identified in tobacco and named NtbZIP01 through to NtbZIP77. These 77 genes were then divided into eleven subfamilies according to their homology with Arabidopsis thaliana. NtbZIPs were unevenly distributed across twenty-two tobacco chromosomes, and we found sixteen pairs of segmental duplication. We further studied the collinearity between these genes and related genes of six other species. Quantitative real-time polymerase chain reaction analysis identified that expression patterns of bZIPs differed, including in different organs and under various abiotic stresses. NtbZIP49 might be important in the development of flowers and fruits; NtbZIP18 might be an important regulator in abiotic stress. Conclusions In this study, the structures and functions of the bZIP family in tobacco were systematically explored. Many bZIPs may play vital roles in the regulation of organ development, growth, and responses to abiotic stresses. This research has great significance for the functional characterisation of the tobacco bZIP family and our understanding of the bZIP family in higher plants. </jats:sec

The complete chloroplast genome sequence of Urtica fissa

Urtica fissa E. Pritz is not only an important medicinal plant for rheumatism and cough relief, but it is also an important forage plant. In this study, the complete chloroplast genome of U. fissa was assembled for the first time and reported to be 146,837 base pairs (bp) long with a typical tetragonal structure and including a large single-copy of 79,657 bp, a small single-copy of 17,712 bp, and two inverted repeats of 24,734 bp each. It harbors 115 unique genes, including 70 protein-coding genes, 38 transfer RNA genes, and 7 ribosomal RNA genes. Phylogenetic analysis showed that U. fissa is closely related to Urtica lobatifolia. This study contributes to the understanding of the origin and evolution of U. fissa, as well as its genetic relationships with other species

Systematic analysis and expression profiles of TCP gene family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stress

Abstract Background As transcription factors, the TCP genes are considered to be promising targets for crop enhancement for their responses to abiotic stresses. However, information on the systematic characterization and functional expression profiles under abiotic stress of TCPs in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is limited. Results In this study, we identified 26 FtTCPs and named them according to their position on the chromosomes. Phylogenetic tree, gene structure, duplication events, and cis-acting elements were further studied and syntenic analysis was conducted to explore the bioinformatic traits of the FtTCP gene family. Subsequently, 12 FtTCP genes were selected for expression analysis under cold, dark, heat, salt, UV, and waterlogging (WL) treatments by qRT-PCR. The spatio-temporal specificity, correlation analysis of gene expression levels and interaction network prediction revealed the potential function of FtTCP15 and FtTCP18 in response to abiotic stresses. Moreover, subcellular localization confirmed that FtTCP15 and FtTCP18 localized in the nucleus function as transcription factors. Conclusions In this research, 26 TCP genes were identified in Tartary buckwheat, and their structures and functions have been systematically explored. Our results reveal that the FtTCP15 and FtTCP18 have special cis-elements in response to abiotic stress and conserved nature in evolution, indicating they could be promising candidates for further functional verification under multiple abiotic stresses. </jats:sec

Image_1_Genome-wide analysis of the Tritipyrum WRKY gene family and the response of TtWRKY256 in salt-tolerance.pdf

IntroductionThe transcription factor WRKY is widespread in the plant kingdom and plays a crucial role in diverse abiotic stress responses in plant species. Tritipyrum, an octoploid derived from an intergeneric cross between Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), is a valuable germplasm resource for introducing superior traits of Th. elongatum into T. aestivum. The recent release of the complete genome sequences of T. aestivum and Th. elongatum enabled us to investigate the organization and expression profiling of Tritipyrum WRKY genes across the entire genome.ResultsIn this study, 346 WRKY genes, from TtWRKY1 to TtWRKY346, were identified in Tritipyrum. The phylogenetic analysis grouped these genes into three subfamilies (I-III), and members of the same subfamilies shared a conserved motif composition. The 346 TtWRKY genes were dispersed unevenly across 28 chromosomes, with 218 duplicates. Analysis of synteny suggests that the WRKY gene family may have a common ancestor. Expression profiles derived from transcriptome data and qPCR demonstrated that 54 TtWRKY genes exhibited relatively high levels of expression across various salt stresses and recovery treatments. Tel1E01T143800 (TtWRKY256) is extremely sensitive to salt stress and is on the same evolutionary branch as the salt-tolerant A. thaliana genes AtWRKY25 and AtWRKY33. From 'Y1805', the novel AtWRKY25 was cloned. The Pearson correlation analysis identified 181 genes that were positively correlated (R>0.9) with the expression of TtWRKY256, and these genes were mainly enriched in metabolic processes, cellular processes, response to stimulus, biological regulation, and regulation of biological. Subcellular localization and qRT-PCR analysis revealed that TtWRKY256 was located in the nucleus and was highly expressed in roots, stems, and leaves under salt stress.DiscussionThe above results suggest that TtWRKY256 may be associated with salt stress tolerance in plants and may be a valuable alien gene for improving salt tolerance in wheat.</p

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

AbstractBackgroundTranscription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. Thetrihelixgene has been systematically studied in some dicots and monocots, includingArabidopsis,tomato, chrysanthemum, soybean, wheat, corn, rice, and buckwheat. However, there are no related studies on sorghum.ResultsIn this study, a total of 40 sorghum trihelix (SbTH) genes were identified based on the sorghum genome, among which 34 were located in the nucleus, 5 in the chloroplast, 1 (SbTH38) in the cytoplasm, and 1 (SbTH23) in the extracellular membrane. Phylogenetic analysis of theSbTHgenes andArabidopsisand ricetrihelixgenes indicated that the genes were clustered into seven subfamilies: SIP1, GTγ, GT1, GT2, SH4, GTSb8, and orphan genes. TheSbTHgenes were located in nine chromosomes and none on chromosome 10. One pair of tandem duplication gene and seven pairs of segmental duplication genes were identified in theSbTHgene family. By qPCR, the expression of 14 SbTH members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. Except for the leaves in which the genes were upregulated after only 2 h exposure to high temperature, the 12 SbTHgenes were significantly upregulated in the stems of sorghum seedlings after 24 h under the other abiotic stress conditions. Among the selected genes,SbTH10/37/39were significantly upregulated, whereasSbTH32was significantly downregulated under different stress conditions.ConclusionsIn this study, we identified 40 trihelix genes in sorghum and found that gene duplication was the main force drivingtrihelixgene evolution in sorghum. The findings of our study serve as a basis for further investigation of the functions ofSbTHgenes and providing candidate genes for stress-resistant sorghum breeding programmes and increasing sorghum yield.</jats:sec

Non-additive expression genes play a critical role in leaf vein ratio heterosis in Nicotiana tabacum L.

Abstract Heterosis, recognized for improving crop performance, especially in the first filial (F1) generation, remains an area of significant study in the tobacco industry. The low utilization of leaf veins in tobacco contributes to economic inefficiency and resource waste. Despite the positive impacts of heterosis on crop genetics, investigations into leaf-vein ratio heterosis in tobacco have been lacking. Understanding the mechanisms underlying negative heterosis in leaf vein ratio at the molecular level is crucial for advancing low vein ratio leaf breeding research. This study involved 12 hybrid combinations and their parental lines to explore heterosis associated with leaf vein ratios. The hybrids displayed diverse patterns of positive or negative leaf vein ratio heterosis across different developmental stages. Notably, the F1 hybrid (G70 × Qinggeng) consistently exhibited substantial negative heterosis, reaching a maximum of -19.79% 80 days after transplanting. A comparative transcriptome analysis revealed that a significant proportion of differentially expressed genes (DEGs), approximately 39.04% and 23.73%, exhibited dominant and over-dominant expression patterns, respectively. These findings highlight the critical role of non-additive gene expression, particularly the dominance pattern, in governing leaf vein ratio heterosis. The non-additive genes, largely associated with various GO terms such as response to abiotic stimuli, galactose metabolic process, plant-type cell wall organization, auxin-activated signaling pathway, hydrolase activity, and UDP-glycosyltransferase activity, were identified. Furthermore, KEGG enrichment analysis unveiled their involvement in phenylpropanoid biosynthesis, galactose metabolism, plant hormone signal transduction, glutathione metabolism, MAPK signaling pathway, starch, and sucrose metabolism. Among the non-additive genes, we identified some genes related to leaf development, leaf size, leaf senescence, and cell wall extensibility that showed significantly lower expression in F1 than in its parents. These results indicate that the non-additive expression of genes plays a key role in the heterosis of the leaf vein ratio in tobacco. This study marks the first exploration into the molecular mechanisms governing leaf vein ratio heterosis at the transcriptome level. These findings significantly contribute to understanding leaf vein ratios in tobacco breeding strategies

Additional file 5 of Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L.

Additional file 5: Figure S1. The correlation analysis between 8 different tissues and expression patterns of the 11 Nicotiana tabacum L. bZIP genes