Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica

- By analysing the expression patterns of CsbZIPs in different tissues and under abiotic stresses, 21 CsbZIP genes were differentially expressed between chasmogamous (CH) and cleistogamous (CL) flowers, including two FLOWERING LOCUS D (FD) genes.
- Strikingly, 17 common CsbZIP genes showed differential expression under stress response and during CL flowering.
- songorica and provide abiotic stress-responsive and CL-associated candidate CsbZIP genes for potential applications in the genetic improvement of plants..
- In Arabidopsis and alfalfa, overexpression of the C.
- In this study, 86 predicted CsbZIP genes were identified from the C.
- To further understand the structural evolution of the CsbZIP genes, we analysed the gene structure of the CsbZIP genes.
- Twenty-one CsbZIP genes (24.4%) had one exon, 19 of which were clustered into subfamily A.
- exons, which was the highest number of exons among the CsbZIP genes.
- In subfamilies A, B, E, H, and I, most CsbZIP genes contained <.
- 5 exons, and most of the CsbZIP genes in subfamilies C, D, and G contained 6–11 exons (Additional file 2: Figure S1).
- In summary, the CsbZIP genes have conserved structural and exon- intron organization similarities in the same subfamily..
- Genome synteny and variation analysis of the bZIP family in C.
- For gene loci analysis, 82 CsbZIP genes (95.34%) were lo- cated on 20 C.
- followed by chromo- somes CsA04, CsB08 and CsA02 with approximately 8.5%, but no CsbZIP genes were located on chromosome CsB19 (Additional file 4: Figure S3).
- songorica, the frequency distributions of the relative Ks for the paralogous gene pairs peaked at 0–0.4 in C.
- Additionally, syntenic orthologous gene pairs of one OsbZIP corresponded to multiple CsbZIP genes.
- Strikingly, syntenic orthologous gene pairs with four CsbZIP genes corresponded to the same two genes: CsbZIP63/CsbZIP62/CsbZIP52/CsbZIP46-OsbZIP72/.
- Identification of cis-elements in the CsbZIP promoters and LTR retrotransposon insertions in the CsbZIP introns To explore the mechanisms of the CsbZIP genes in the stress response and developmental process, we searched for 18 cis-elements in the promoter region of the CsbZIP genes, which were predicted to be in- volved in development, abiotic stress and phytohor- mone response.
- Additionally, 30 CsbZIP genes contained the salicylic acid responsive elements (TCA-element), which were involved in the salicylic acid response.
- Notably, the promoters of 13 CsbZIP genes (15.1%) contained at least six cis-elements (Additional file 7: Table S4).
- Subfamily G contained all identified cis-elements in the promoters of the CsbZIP genes.
- Here, 14 CsbZIP genes (16.3%) were identified for the insertion of the LTR retrotransposon in the intron region (Fig.
- Furthermore, 4 CsbZIP genes contained both copia and gypsy elements (Fig.
- To study the expression pattern of the CsbZIP genes in different organs, we performed transcriptome analysis of C.
- Eighty-one (94.2%) CsbZIP genes expressed at least in one tissue (FPKM≥1), and genes.
- 1| CsbZIP genes between CH and CL flowers, including five downregulated and 16 upregulated CsbZIP (Fig.
- Four dimorphic florets related CsbZIP genes (CsbZIP20, CsbZIP57, CsbZIP59 and CsbZIP82) were selected for co- expression analysis (Fig.
- This result suggested that the CsbZIP genes may par- ticipate in dimorphic florets development by regulating floral organ development and flower development..
- Identification of abiotic stress-related CsbZIP genes We used the transcriptome data sets of C.
- songorica treated with high temperature (heat), low temperature (cold), salt and drought stress to determine the impact of the CsbZIP genes on abiotic stress.
- Seventy-four (87.2%) and seventy-eight (90.7%) CsbZIP genes showed gene ex- pression at least in one stress condition (FPKM ≥1) in shoots and roots (Fig.
- Furthermore and CsbZIP genes were differentially expressed |log 2 (fold change.
- 9b and 48 differentially expressed CsbZIP genes were identified in C.
- Compared to the controls, there were and 53 differentially expressed CsbZIP genes in roots under.
- A total of 77 CsbZIP genes were differentially expressed in both shoots and roots under four abiotic stress conditions..
- Ten stress-related CsbZIP genes were found in the co-expressed network analysis.
- 4 Ks and Ka/Ks value distributions of the bZIP genes in the genomes of C.
- We further identified the ABA-dependent and ABA- independent abiotic stress-responsive CsbZIP genes.
- A total of 22 CsbZIP genes were differentially expressed in the ABA treatment.
- Among these genes, eight CsbZIP genes were classed to subfamily A.
- Furthermore, 22 CsbZIP genes were also responsive to both the ABA and.
- 5 Statistical analysis for cis-elements of CsbZIP genes.
- a Proportions of genes with various cis-elements among the CsbZIP genes.
- songorica, while 55 CsbZIP genes were specifically responsive to abiotic stress, indicat- ing that more ABA-independent CsbZIP genes were in- volved in response to abiotic stress..
- The expression patterns of some related CsbZIP genes were verified by RT-qPCR under salt stress (100 mM NaCl.
- 9, the result was relatively consistent with similar trends, indicating that the selected CsbZIP genes were significantly induced by these five stresses.
- The distribution of the CsbZIP genes was not different in the subgenome of C.
- 6 Insertion of the LTR retrotransposon into the CsbZIP intron.
- Strikingly, no CsbZIP genes were distributed in subfamily F, which is involved in Zn transport (Fig.
- Gene structure analysis indicated that the CsbZIP genes introns presented a large difference with numbers ranging from 0 to 10, but there was a similar gene struc- ture in each subfamily (Additional file 2: Figure S1).
- We found that approximately 24% of CsbZIP genes only had an exon and were mainly clustered in subfamily S, with.
- The CsbZIP genes of subfamilies D, C and G had more exons than all other subfamilies (Additional file 2: Figure S1).
- 7 Expression and co-expression network analysis of the CsbZIP genes in CH and CL flowers.
- a Heat map of all CsbZIP genes in different tissues based on transcriptome datasets.
- b Venn diagram showing overlap of highly expressed CsbZIP genes (FPKM ≥ 20) in different tissues.
- c Number of differentially expressed CsbZIP genes between CH and CL flowers.
- d Co-expression network of CsbZIP genes with DEGs between CH and CL flowers.
- of bZIP transcription factors is depend on the basic re- gion of the bZIP domain.
- In this study, some cis-act- ing elements also were identified in the upstream of CsbZIP genes.
- songorica, 84% CsbZIP genes contained at least one.
- Together, gene structure and conserved motif analysis indicated that the relationship of CsbZIP genes in the same subfamily were closer than those in other subfamilies during the gene evolution process..
- 8 Expression and co-expression network analysis of CsbZIP genes under abiotic stress.
- a Heat map of all CsbZIP genes under different abiotic stresses based on transcriptome datasets.
- b Venn diagram showing the overlap of differentially expressed CsbZIP genes under abiotic stress.
- c Co-expression network of the CsbZIP genes with DEGs under abiotic stress.
- d Venn diagram showing the overlap of differentially expressed CsbZIP genes under abiotic stress and ABA stress.
- These results suggested that the expansion of the C.
- OsbZIP and 73 CsbZIP genes (84.9%) were identified as orthologs.
- Most gene pairs (88.3%) showed a substantially complex re- lationship, including single CsbZIP genes correspond- ing to the multiple OsbZIP genes or single OsbZIP genes corresponding to the multiple CsbZIP genes..
- 9 Confirmation of the expression patterns of the CsbZIP genes under abiotic stress in shoots using quantitative qRT-PCR.
- Here, 79.1 and 87.2% abiotic stress-related CsbZIP genes were identified in shoots and roots, respectively.
- These results indi- cated that CsbZIP genes are involved in the regulation of abiotic stresses.
- Gene expression analysis demonstrated that there were more stress-responsive CsbZIP genes for drought and heat than for cold and salt stress-responsive CsbZIP genes, suggesting that CsbZIP genes might have im- portant biological functions in response to drought and high temperature.
- Further- more, all ABA-responsive CsbZIP genes were differentially expressed under abiotic stresses.
- These results indicate that the CsbZIP genes participate in ABA-dependent and ABA-independent pathways..
- The WGCNA analysis showed that some stress- responsive CsbZIP genes were co-expressed with genes involved in flower development.
- Additionally, some CL flower-related CsbZIP genes were also co-expressed with genes that responded to stress (Fig.
- We further found that 17 common CsbZIP genes showed differential expression under stress response and during CL flowering, revealing that these genes may involve nu- merous developmental processes in C.
- Four CsbZIP genes were selected to verify the expression pattern in CL flowers and CH flowers and under abiotic stress by RT-qPCR.
- CL flower development and stress response CsbZIP genes were highlighted for their expression patterns and expression networks.
- These results may provide useful insights into the CsbZIP genes in the stress response and CL flower develop- ment in future studies..
- Identification of the bZIP genes in C.
- The online tool GSDS was used to show the gene structure of CsbZIP genes (http://.
- Identification of putative cis-elements and LTR retrotransposon in CsbZIP genes.
- The 1500 bp upstream sequences of the CsbZIP genes were used to identify the cis-elements in the promoter.
- 10 Model of functional divergence of CL flowering-related and stress-responsive CsbZIP genes in C.
- Confirmation of the expression patterns of the CsbZIP genes using quantitative qRT-PCR.
- LTR-FINDER (1.0.5 version) was used to identify the LTR retrotransposon in CsbZIP genes (http://tlife.fudan..
- Transcriptome data of CsbZIP genes under drought stress were obtained from our previous study [65]..
- Finally, a heat map of the CsbZIP genes expression profile was shown by the OmicShare tools, a free online platform for data analysis (http://www.omicshare.com/.
- Expression profiles of CsbZIP genes in different tissues of C.
- The co-expression network analysis of CsbZIP genes in- volved in CL flower development and stress response were performed with weighted gene co-expression network (WGCNA.
- Basic characteristic of CsbZIP genes in C..
- Gene structure and conserved motif of CsbZIP genes based on the evolutionary relationship.
- Cis-elememts analysis of CsbZIP genes..
- Expression pattern of CsbZIP genes in different organ..
- Transcriptome data of CsbZIP genes in shoot and root under abiotic stress..
- Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice.
- Genome-wide analysis of the bZIP transcription factors in cucumber.
- Comparative analysis of the receptor-like kinase family in Arabidopsis and rice

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