Genome-wide analysis and characterization of heat shock transcription factors (Hsfs) in common bean (Phaseolus vulgaris L.)

Cloning and expression analysis of RhHsf24 gene in Rose (Rosa hybrida)

Rose (Rosa hybrida) is one of the most important ornamental and perfume industry crops worldwide, both economically and culturally. Abiotic stresses, such as high temperature and salt are crucial factors influencing the quality of roses. In this study, RhHsf24 was isolated from rose (R. hybrida 'Samantha'), which encodes 295 amino acids (aa). Sequence comparison with members of Arabidopsis Hsfs family revealed that this gene is most closely related to AtHsfB1; phylogenetic tree analysis with proteins from other species showed that it clusters with R. rugosa (RrHSF24), Fragaria vesca (FvHSFB1a) and Argentina anserina (AaHSF24), which are the closest relatives and belong to the class B heat shock transcription factors. RhHsf24 was localized in the nucleus. The qRT-PCR results indicated that the gene was expressed in roots, stems, leaves, flowers and buds. Expression analysis of the gene in leaves subjected to various temperatures and durations of heat stress treatment demonstrated that RhHsf24 gene expression is induced by heat stress. Under salt stress, the expression of the RhHsf24 gene generally exhibited a high level of expression with increasing concentration. The above results preliminarily clarified the biological function of RhHsf24, and provide a genetic resource and theoretical reference for the resistance breeding of roses.

Genome-Wide Identification and Expression Analysis of the HSF Gene Family in Ammopiptanthus mongolicus

Ammopiptanthus mongolicus is an ancient remnant species from the Mediterranean displaying characteristics such as high-temperature tolerance, drought resistance, cold resistance, and adaptability to impoverished soil. In the case of high-temperature tolerance, heat shock transcription factors (HSFs) are integral transcriptional regulatory proteins exerting a critical role in cellular processes. Despite extensive research on the HSF family across various species, there has been no analysis specifically focused on A. mongolicus. In this study, we identified 24 members of the AmHSF gene family based on the genome database of A. mongolicus, which were unevenly distributed over 9 chromosomes. Phylogenetic analysis showed that these 24 members can be categorized into 5 primary classes consisting of a total of 13 subgroups. Analysis of the physical and chemical properties revealed significant diversity among these proteins. With the exception of the AmHSFB3 protein, which is localized in the cytoplasm, all other AmHSF proteins were found to be situated in the nucleus. Comparison of amino acid sequences revealed that all AmHSF proteins contain a conserved DNA-binding domains structure, and the DNA-binding domains and oligomerization domains of the AmHSF gene exhibit conservation with counterparts across diverse species; we investigated the collinearity of AmHSF genes in relation to those of three other representative species. Through GO enrichment analysis, evidence emerged that AmHSF genes are involved in heat stress responses and may be involved in multiple transcriptional regulatory pathways that coordinate plant growth and stress responses. Finally, through a comprehensive analysis using transcriptome data, we examined the expression levels of 24 AmHSFs under 45 °C. The results revealed significant differences in the expression profiles of AmHSFs at different time intervals during exposure to high temperatures, highlighting their crucial role in responding to heat stress. In summary, these results provide a better understanding of the role and regulatory mechanisms of HSF in the heat stress response of A. mongolicus, meanwhile also establishing a foundation for further exploration of the biological functions of AmHSF in the adversity response of A. mongolicus.

Genome-Wide Identification and Functional Analysis of RF2 Gene Family and the Critical Role of GhRF2-32 in Response to Drought Stress in Cotton

Cotton is an important natural fiber crop. The RF2 gene family is a member of the bZIP transcription factor superfamily, which plays an important role in plant resistance to environmental stresses. In this paper, the RF2 gene family of four cotton species was analyzed genome-wide, and the key gene RF2-32 was cloned for functional verification. A total of 113 RF2 genes were identified in the four cotton species, and the RF2 family was relatively conserved during the evolution of cotton. Chromosome mapping and collinear analysis indicated that fragment replication was the main expansion mode of RF2 gene family during evolution. Cis-element analysis showed that there were many elements related to light response, hormone response and abiotic stress response in the promoters of RF2 genes. The transcriptome and qRT-PCR analysis of RF2 family genes in upland cotton showed that RF2 family genes responded to salt stress and drought stress. GhRF2-32 protein was localized in the cell nucleus. Silencing the GhRF2-32 gene showed less leaf wilting and increased total antioxidant capacity under drought and salt stress, decreased malondialdehyde content and increased drought and salt tolerance. This study revealed the evolutionary and functional diversity of the RF2 gene family, which laid a foundation for the further study of stress-resistant genes in cotton.

Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]

Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe²⁺ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.

Analysis of the C2H2 Gene Family in Maize (Zea mays L.) under Cold Stress: Identification and Expression

The C2H2 zinc finger protein is one of the most common zinc finger proteins, widely exists in eukaryotes, and plays an important role in plant growth and development, as well as in salt, low-temperature, and drought stress and other abiotic stress responses. In this study, C2H2 members were identified and analyzed from the low-temperature tolerant transcriptome sequencing data of maize seedlings. The chromosome position, physical and chemical properties, evolution analysis, gene structure, conservative motifs, promoter cis elements and collinearity relationships of gene the family members were analyzed using bioinformatics, and the expression of the ZmC2H2 gene family under cold stress was analyzed by fluorescent quantitative PCR. The results showed that 150 members of the C2H2 zinc finger protein family were identified, and their protein lengths ranged from 102 to 1223 bp. The maximum molecular weight of the ZmC2H2s was 135,196.34, and the minimum was 10,823.86. The isoelectric point of the ZmC2H2s was between 33.21 and 94.1, and the aliphatic index was 42.07-87.62. The promoter cis element analysis showed that the ZmC2H2 family contains many light-response elements, plant hormone-response elements, and stress-response elements. The analysis of the transcriptome data showed that most of the ZmC2H2 genes responded to cold stress, and most of the ZmC2H2 genes were highly expressed in cold-tolerant materials and lowly expressed in cold-sensitive materials. The real-time quantitative PCR (qRT-PCR) analysis showed that ZmC2H2-69, ZmC2H2-130, and ZmC2H2-76 were significantly upregulated, and that ZmC2H2-149, ZmC2H2-33, and ZmC2H2-38 were significantly downregulated. It is hypothesized that these genes, which function in different metabolic pathways, may play a key role in the maize cold response. These genes could be further studied as candidate genes. This study provides a theoretical reference for further study on the function analysis of the maize C2H2 gene family.

Functional Characterization of Heat Shock Factor (CrHsf) Families Provide Comprehensive Insight into the Adaptive Mechanisms of Canavalia rosea (Sw.) DC. to Tropical Coral Islands

Heat shock transcription factors (Hsfs) are key regulators in plant heat stress response, and therefore, they play vital roles in signal transduction pathways in response to environmental stresses, as well as in plant growth and development. Canavalia rosea (Sw.) DC. is an extremophile halophyte with good adaptability to high temperature and salt-drought tolerance, and it can be used as a pioneer species for ecological reconstruction on tropical coral islands. To date, very little is known regarding the functions of Hsfs in the adaptation mechanisms of plant species with specialized habitats, especially in tropical leguminous halophytes. In this study, a genome-wide analysis was performed to identify all the Hsfs in C. rosea based on whole-genome sequencing information. The chromosomal location, protein domain or motif organization, and phylogenetic relationships of 28 CrHsfs were analyzed. Promoter analyses indicated that the expression levels of different CrHsfs were precisely regulated. The expression patterns also revealed clear transcriptional changes among different C. rosea tissues, indicating that the regulation of CrHsf expression varied among organs in a developmental or tissue-specific manner. Furthermore, the expression levels of most CrHsfs in response to environmental conditions or abiotic stresses also implied a possible positive regulatory role of this gene family under abiotic stresses, and suggested roles in adaptation to specialized habitats such as tropical coral islands. In addition, some CrHsfAs were cloned and their possible roles in abiotic stress tolerance were functionally characterized using a yeast expression system. The CrHsfAs significantly enhanced yeast survival under thermal and oxidative stress challenges. Our results contribute to a better understanding of the plant Hsf gene family and provide a basis for further study of CrHsf functions in environmental thermotolerance. Our results also provide valuable information on the evolutionary relationships among CrHsf genes and the functional characteristics of the gene family. These findings are beneficial for further research on the natural ecological adaptability of C. rosea to tropical environments.