Identification and characterization of the bZIP transcription factor family and its expression in response to abiotic stresses in sesame

Abstract

Basic leucine zipper (bZIP) gene family is one of the largest transcription factor families in plants, and members of this family play important roles in multiple biological processes such as light signaling, seed maturation, flower development as well as abiotic and biotic stress responses. Nonetheless, genome-wide comprehensive analysis of the bZIP family is lacking in the important oil crop sesame. In the present study, 63 bZIP genes distributed on 14 linkage groups were identified in sesame, and denominated as SibZIP01-SibZIP63. Besides, all members of SibZIP family were divided into nine groups based on the phylogenetic relationship of Arabidopsis bZIPs, which was further supported by the analysis of their conserved motifs and gene structures. Promoter analysis showed that all SibZIP genes harbor cis-elements related to stress responsiveness in their promoter regions. Expression analyses of SibZIP genes based on transcriptome data showed that these genes have different expression patterns in different tissues. Additionally, we showed that a majority of SibZIPs (85.71%) exhibited significant transcriptional changes in responses to abiotic stresses, including drought, waterlogging, osmotic, salt, and cold, suggesting that SibZIPs may play a cardinal role in the regulation of stress responses in sesame. Together, these results provide new insights into stress-responsive SibZIP genes and pave the way for future studies of SibZIPs-mediated abiotic stress response in sesame.

In Silico Identification and Expression Analysis of Nuclear Factor Y (Nf-Y) Transcription Factors in Cucumber

“…wur.nl/en/show/Mapchart.htm) as previously described [33]. Duplication analysis was conducted using MCScanX software (http://chibba.pgml.uga.edu/mcscan2), and tandem and segmental duplication events were determined based on the previous description [34]. For sequence alignment of cucumber NF-Y proteins, their amino acid sequences were aligned using MAFFT (https://www.ebi.ac.uk/Tools/msa/mafft/) with default settings and visualized with GeneDoc.…”

“…To identify potential segmental and tandem duplications within the cucumber genome, we assessed the duplication events among the identified CsaNF-Y genes using the criteria from a previous study [34]. Tandem duplication was detected for one pair of CsaNF-Y genes, CsaNF-YB6 and CsaNF-YB7, whereas segmental duplication was found for four pairs of genes, including CsaNF-YA1 and CsaNF-YA5, CsaNF-YA1 and CsaNF-YA7, CsaNF-YB5 and CsaNF-YB11, and CsaNF-YB8 and CsaNF-YB10 ( Figure 2).…”

“…Furthermore, the core histone structures including the HFM (histone fold motif) of the core histone H2B and H2A were present in CsaNF-YB and CsaNF-YC proteins, respectively ( Figure 3B,C). CsaNF-YB proteins contained a DNA-binding domain, a NF-YA interaction domain, and a NF-YC interaction domain, and the region of the NF-YC interaction domain was so long that it overlapped with the NF-YA interaction and DNA-binding domains To identify potential segmental and tandem duplications within the cucumber genome, we assessed the duplication events among the identified CsaNF-Y genes using the criteria from a previous study [34]. Tandem duplication was detected for one pair of CsaNF-Y genes, CsaNF-YB6 and CsaNF-YB7, whereas segmental duplication was found for four pairs of genes, including CsaNF-YA1 and CsaNF-YA5, CsaNF-YA1 and CsaNF-YA7, CsaNF-YB5 and CsaNF-YB11, and CsaNF-YB8 and CsaNF-YB10 (Figure 2).…”

Transcription Factors and microRNA Genes Regulatory Network Construction Under Drought Stress in Sesame (Sesamum indicum L.)

“…The development of high-throughput technologies in recent years and their combination with bioinformatics analysis enabled the researchers to have a clearer vision of drought response mechanisms in plants and helped them to identify the drought tolerance candidate genes more efficiently for use in the breeding program. Recently, studies on the role of transcription factors in Sesame responses to drought stress were increased and have been growing [14,24,25,26].…”

The Analysis of Pinus pinaster SnRKs Reveals Clues of the Evolution of This Family and a New Set of Abiotic Stress Resistance Biomarkers

“…This conservation makes highly probable the involvement of the P. pinaster kinases with these signaling elements. SnRK1-2 related bZIP transcription factors are involved in plant abiotic and energetic stress responses in different plant species [41,42]. The overexpression of the Arabidopsis bZIP ABF2 confers tolerance to multiple abiotic stresses [43].…”