Genome-wide identification, evolution and expression pattern analysis of the GATA gene family in Sorghum bicolor

Molecular mechanisms underlying abiotic stress responses in buckwheat

Plants have endured evolutionary changes for hundreds of years under the impact of increasing abiotic and biotic stress due to increasing human activities over the past centuries. Scientists have been working to understand the molecular mechanisms of plant responses to severe environmental stress, as plants have complex molecular arrangements to respond and adapt to abiotic stress, including drought, cold, and heat stress. Buckwheat (Fagopyrum spp.) is a resilient pseudocereal known for its nutritional value and adaptability to various environmental conditions, making it an essential crop in sustainable agriculture. It is particularly noted for its gluten-free nature and high-quality protein content, which benefit those with gluten sensitivities. However, recent studies revealed that buckwheat cultivation faces significant challenges from abiotic stressors such as drought, salinity, temperature extremes, and heavy metal toxicity, which can adversely affect its growth and yield. We have acknowledged key genes and factors in regulating complex responses and tolerance of plants in response to abiotic stresses. We compiled new data about diverse mechanisms by which different Fagopyrum species manage abiotic stress, encompassing physiological, biochemical, and molecular adaptations. As global food production demands rise, effective management strategies for these stress factors are increasingly critical for optimising buckwheat production and ensuring food security in a changing climate.

Systematic expression analysis of pecan GATA gene family during graft healing reveals that CiGATA8b and CiGATA12a are involved in stress responses

GATA transcription factors are type IV zinc-finger proteins that could bind to the GATA motif within the promoters of downstream genes, thus influencing plant development and stress responses. Presently, pecan GATA (CiGATA) gene family has yet to be systematically characterized. In this study, 33 CiGATA members were identified and grouped into four classes, with genes within the same class exhibiting structural commonality. Cis-Elements in the promoters of CiGATAs were predicted to be mainly associated with light, abscisic acid, methyl jasmonate, and anaerobic induction. Four members including CiGATA8b/12a/1b/3b were highly responsive to graft healing, among which CiGATA8b and CiGATA12a were likely related to the stress responses during graft healing, as revealed by the annotation of their co-expressed genes. CiGATA8b and CiGATA12a were both located in the nucleus and acted as transcriptional suppressor and activator, respectively. Yeast one-hybrid indicated that CiGATA8b and CiGATA12a could bind to the promoters of CiNLR and CiNAC30, respectively. Functional characterization via virus-induced gene silencing and overexpression revealed that CiGATA8b could increase disease resistance, and CiGATA12a was able to alleviate oxidative damage. Our results suggest that CiGATA8b and CiGATA12a are associated with stress responses, laying a foundation for understanding the molecular mechanisms of graft healing in pecan.

Genome-wide identification and gene expression pattern analysis of the carotenoid cleavage oxygenase gene family in Fagopyrum tataricum

BACKGROUND

Carotenoid cleavage oxygenases (CCOs) convert carotenoids into volatile aromatic compounds implicated in plant growth and development. They affect the synthesis of hormones, including abscisic acid (ABA) and strigolactone (SL). However, the CCO family in Tartary buckwheat remains unelucidated.

RESULTS

We identified the FtCCO gene family based on Tartary buckwheat genomic data and analyzed the biological function of the FtCCO genes using bioinformatics methods and the expression pattern of the gene using fluorescence quantitative PCR. Three pairs of fragment duplication genes were found in FtCCOs, and the motifs were highly conserved within the same subfamily. FtCCO genes are closely related to the dicotyledonous Arabidopsis thaliana, which has the highest number of co-linear genes. The qRT-PCR showed that among the tissue-specific expression patterns of Tartary buckwheat CCO genes, the expression of the FtCCOs was higher in the leaves. In Tartary buckwheat grain development, the relative expression of most FtCCOs was higher at the later stage. The relative expression of many genes was higher in the stems under cold, dark, NaCl, and abiotic stress conditions. However, under the hormone and plant growth regulator treatments, the expression of the nine FtCCOs was relatively low in the stems. Notably, the relative expression of FtNCED4 was extremely high under abiotic stress and hormone induction, indicating that FtNCED4 may be involved in the growth and development of Tartary buckwheat. In this study, the FtCCO family genes of Tartary buckwheat were identified at the genome-wide level, and the gene expression pattern of the FtCCO gene family in different tissues or treatments was determined. This study provides a theoretical basis for further analysis of the functions of theFtCCO family, which is of great significance for the mining of resistance genes and trait improvement.

Identification of nuclear factor YA6 genes in sorghum and characterization of their involvement in drought tolerance

Nuclear factor Y alpha proteins (NF-YAs) are conserved transcription factor proteins crucial to plant growth and development that exhibit specific responses to biotic and abiotic stresses. Using bioinformatics approaches to investigate the NF-YA family in sorghum (Sorghum bicolor), we identified nine SbNF-YA genes unevenly distributed on four of the 10 sorghum chromosomes. Despite variations in gene structure, all encode proteins have the characteristic CBFB_NFYA domain and other predicted motifs. The secondary structure of SbNF-YA members is predominantly composed of α-helices and random coils. A phylogenetic analysis of NF-YAs of sorghum and other plant species indicated that SbNF-YAs are closely related to NF-YAs from maize (Zea mays) and distantly related to those in Arabidopsis (Arabidopsis thaliana). A colinearity analysis determined that six of the nine SbNF-YA genes arose from segmental duplication events. Transcriptome and RT-qPCR analyses showed that the expression levels of eight of the SbNF-YA genes (SbNF-YA5 being the exception) are responsive to drought stress to varying degrees. Notably, SbNF-YA1, SbNF-YA4, SbNF-YA6, SbNF-YA8, and SbNF-YA9 expression was significantly upregulated under the stress conditions, suggesting that they participate in drought response. When heterologously expressed in Arabidopsis, SbNF-YA6 conferred greater tolerance of drought stress imposed by treatment with the osmolyte mannitol, with the transgenic Arabidopsis lines showing superior germination rates; longer roots; higher fresh weight; higher activities of the enzymes peroxidase, superoxide dismutase, and catalase; and higher soluble protein and proline contents, compared to the wild type. Additionally, the transgenic Arabidopsis lines accumulated lower levels of hydrogen peroxide, superoxide anion, and malondialdehyde. The expression levels of several drought-responsive genes were elevated in transgenic Arabidopsis seedlings relative to the wild type, indicating that the heterologous expression of SbNF-YA6 enhances the drought tolerance of Arabidopsis.

Genome-wide identification, evolution, and expression level analysis of the TALE gene family in Sorghum bicolor

BACKGROUND

The three-amino-acid-loop-extension (TALE) is a ubiquitous homeodomain transcription factor among plant species involved in regulating plant growth, development, and environmental responses. However, this has not been systematically analyzed or reported in sorghum.

RESULTS

In this study, 23 SbTALE genes were identified using bioinformatics and other methods at the genome level of sorghum, classified into two families, KNOX and BEL1-like family, and localized on ten chromosomes. One pair of tandem duplicated and seven pairs of segmentally duplicated genes were found, and the conserved motifs of SbTALEs among the same subfamilies were highly conserved, with highly conserved gene structures. SbTALEs genes have the most collinear genes with monocotyledonous Zea mays and are more closely related; SbTALEs have undergone purification and diversification selection in the evolutionary process. Overall, except for SbTALE21 and SbTALE23, the expression of the other six SbTALEs was higher in the stems, whereas the expression of SbTALE21 and SbTALE23 was higher in the leaves. In sorghum grain development, the lowest relative expression of SbTALEs was observed in grains in the late stage, and the expression of SbTALE21 was higher in grains in the early stage and husks in the late stage. In addition, SbTALE14 and SbTALE21 showed higher expression in the roots and stems under the cold treatment, and SbTALE02 and SbTALE12 showed higher expression in the roots and stems under the PEG treatment. Under the four hormone treatments, the expression of eight SbTALEs was relatively low in stems, the expression of SbTALE13 was higher in leaves than in roots and stems, and the expression of SbTALE23 was higher under the MeJA and SA treatments.

CONCLUSION

This study lays a theoretical foundation for the study of the biological function and mechanism of SbTALE genes and is of great significance for the mining of resistance genes and trait improvement.

Comparative analysis of amino acid sequence level in plant GATA transcription factors

Transcription factors (TFs) are essential regulators of gene expression, influencing numerous biological processes such as development, growth, and cellular responses in plants. Among these, GATA TFs are distinguished by their highly conserved DNA-binding domain, characterized by a class IV zinc finger motif (CX2CX18-20CX2C). This study investigates the amino acid sequence patterns of 5,335 GATA TFs across 165 plant species sourced from the PlantTFDB database ( http://planttfdb.gao-lab.org/ ), encompassing diverse taxonomic groups. Through comparative sequence analysis, I identify conserved domains and structural features that enhance the understanding functional roles, evolutionary conservation, and lineage-specific adaptations of GATA TFs. These findings provide valuable insights into the diversification and functional specialization of GATA TFs, with implications for improving stress tolerance and adaptability in crops. This study contributes to the broader knowledge of transcriptional regulation in plant biology.

Genome-wide identification of the GATA gene family in melon (Cucumis melo) and analysis of their expression characteristics under biotic and abiotic stresses

GATA transcription factors are an important class of transcription factors in plants, known for their roles in tissue development, signal transduction, and responses to biotic and abiotic stresses. To date, there have been no reports on the GATA gene family in melon (Cucumis melo). In this study, 24 CmGATA genes were identified from the melon genome. These family members exhibit significant differences in protein length, molecular weight, and theoretical isoelectric point and are primarily located in the nucleus. Based on the classification of Arabidopsis thaliana GATA members, the phylogenetic tree divided them into four groups: group I, group II, group III, and group IV, containing 10, 8, 4, and 2 genes, respectively. Notably, CmGATA genes within the same group have highly conserved protein motifs and similar exon-intron structures. The CmGATA family members are unevenly distributed across 10 chromosomes, with six pairs of segmentally duplicated genes and one pair of tandemly duplicated genes, suggesting that gene duplication may be the primary factor in the expansion of the CmGATA family. Melon shares 21, 4, 38, and 34 pairs of homologous genes with A. thaliana, Oryza sativa, Cucumis sativus, and Citrullus lanatus, respectively. The promoter regions are enriched with various cis-acting elements related to growth and development (eight types), hormone regulation (nine types), and stress responses (six types). Expression patterns indicate that different CmGATA family members are significantly expressed in seeds, roots, stems, leaves, tendrils, mesocarp, and epicarp, exhibiting distinct tissue-specific expression characteristics. Quantitative fluorescence analysis revealed that five genes, CmGATA3, CmGATA7, CmGATA16, CmGATA22, and CmGATA24, may be highly active under 48-h drought stress, while CmGATA1 and CmGATA22 may enhance melon resistance to heavy metal lead stress. Additionally, CmGATA22 and CmGATA24 are suggested to regulate melon resistance to Fusarium wilt infection. CmGATA22 appears to comprehensively regulate melon responses to both biotic and abiotic stresses. Lastly, potential protein interaction networks were predicted for the CmGATA family members, identifying CmGATA8 as a potential hub gene and predicting 2,230 target genes with enriched GO functions. This study preliminarily explores the expression characteristics of CmGATA genes under drought stress, heavy metal lead stress, and Fusarium wilt infection, providing a theoretical foundation for molecular mechanisms in melon improvement and stress resistance.

Genome-Wide Analysis and Expression Profiling of Soybean RbcS Family in Response to Plant Hormones and Functional Identification of GmRbcS8 in Soybean Mosaic Virus

Rubisco small subunit (RbcS), a core component with crucial effects on the structure and kinetic properties of the Rubisco enzyme, plays an important role in response to plant growth, development, and various stresses. Although Rbcs genes have been characterized in many plants, their muti-functions in soybeans remain elusive. In this study, a total of 11 GmRbcS genes were identified and subsequently divided into three subgroups based on a phylogenetic relationship. The evolutionary analysis revealed that whole-genome duplication has a profound effect on GmRbcSs. The cis-acting elements responsive to plant hormones, development, and stress-related were widely found in the promoter region. Expression patterns based on the RT-qPCR assay exhibited that GmRbcS genes are expressed in multiple tissues, and notably Glyma.19G046600 (GmRbcS8) exhibited the highest expression level compared to other members, especially in leaves. Moreover, differential expressions of GmRbcS genes were found to be significantly regulated by exogenous plant hormones, demonstrating their potential functions in diverse biology processes. Finally, the function of GmRbcS8 in enhancing soybean resistance to soybean mosaic virus (SMV) was further determined through the virus-induced gene silencing (VIGS) assay. All these findings establish a strong basis for further elucidating the biological functions of RbcS genes in soybeans.

Genome-wide identification, characterization and expression analysis of the bZIP transcription factors in garlic (Allium sativum L.)

Introduction

The bZIP genes (bZIPs) are essential in numerous biological processes, including development and stress responses. Despite extensive research on bZIPs in many plants, a comprehensive genome-wide analysis of bZIPs in garlic has yet to be undertaken.

Methods

In this study, we identified and classified 64 AsbZIP genes (AsbZIPs) into 10 subfamilies. A systematic analysis of the evolutionary characteristics of these AsbZIPs, including chromosome location, gene structure, conserved motifs, and gene duplication, was conducted. Furthermore, we also examined the nucleotide diversity, cis-acting elements, and expression profiles of AsbZIPs in various tissues and under different abiotic stresses and hormone treatments.

Results and Discussion

Our findings revealed that gene replication plays a crucial role in the expansion of AsbZIPs, with a minor genetic bottleneck observed during domestication. Moreover, the identification of cis-acting elements suggested potential associations of AsbZIPs with garlic development, hormone, and stress responses. Several AsbZIPs exhibited tissue-preferential and stress/hormone-responsive expression patterns. Additionally, Asa7G01972 and Asa7G01379 were notably differentially expressed under various stresses and hormone treatments. Subsequent yeast two-hybridization and yeast induction experiments validated their interactions with Asa1G01577, a homologue of ABI5, reinforcing their importance in hormone and abiotic stress responses. This study unveiled the characteristics of the AsbZIP superfamily and lays a solid foundation for further functional analysis of AsbZIP in garlic.

Genome-Wide Identification and Expression Pattern Analysis of GATA Gene Family in Orchidaceae

The GATA transcription factors play crucial roles in plant growth, development, and responses to environmental stress. Despite extensive studies of GATA genes in many plants, their specific functions and mechanisms in orchids remain unexplored. In our study, a total of 149 GATA genes were identified in the genomes of seven sequenced orchid species (20 PeqGATAs, 23 CgGATAs, 24 CeGATAs, 23 DcaGATAs, 20 DchGATAs, 27 DnoGATAs, and 12 GelGATAs), classified into four subfamilies. Subfamily I typically contains genes with two exons, while subfamily II contains genes with two or three exons. Most members of subfamilies III and IV have seven or eight exons, with longer introns compared to subfamilies I and II. In total, 24 pairs (CgGATAs-DchGATAs), 27 pairs (DchGATAs-DnoGATAs), and 14 pairs (DnoGATAs-GelGATAs) of collinear relationships were identified. Cis-acting elements in GATA promoters were mainly enriched in abscisic acid (ABA) response elements and methyl jasmonate (MeJA) elements. Expression patterns and RT-qPCR analysis revealed that GATAs are involved in the regulation of floral development in orchids. Furthermore, under high-temperature treatment, GL17420 showed an initial increase followed by a decrease, GL18180 and GL17341 exhibited a downregulation followed by upregulation and then a decrease, while GL30286 and GL20810 displayed an initial increase followed by slight inhibition and then another increase, indicating diverse regulatory mechanisms of different GATA genes under heat stress. This study explores the function of GATA genes in orchids, providing a theoretical basis and potential genetic resources for orchid breeding and stress resistance improvement.

The Putative GATA Transcription Factor SbGATA22 as a Novel Regulator of Dhurrin Biosynthesis

Cyanogenic glucosides are specialized metabolites produced by over 3000 species of higher plants from more than 130 families. The deployment of cyanogenic glucosides is influenced by biotic and abiotic factors in addition to being developmentally regulated, consistent with their roles in plant defense and stress mitigation. Despite their ubiquity, very little is known regarding the molecular mechanisms that regulate their biosynthesis. The biosynthetic pathway of dhurrin, the cyanogenic glucoside found in the important cereal crop sorghum (Sorghum bicolor (L.) Moench), was described over 20 years ago, and yet no direct regulator of the biosynthetic genes has been identified. To isolate regulatory proteins that bind to the promoter region of the key dhurrin biosynthetic gene of sorghum, SbCYP79A1, yeast one-hybrid screens were performed. A bait fragment containing 1204 base pairs of the SbCYP79A1 5' regulatory region was cloned upstream of a reporter gene and introduced into Saccharomyces cerevisiae. Subsequently, the yeast was transformed with library cDNA representing RNA from two different sorghum developmental stages. From these screens, we identified SbGATA22, an LLM domain B-GATA transcription factor that binds to the putative GATA transcription factor binding motifs in the SbCYP79A1 promoter region. Transient assays in Nicotiana benthamiana show that SbGATA22 localizes to the nucleus. The expression of SbGATA22, in comparison with SbCYP79A1 expression and dhurrin concentration, was analyzed over 14 days of sorghum development and in response to nitrogen application, as these conditions are known to affect dhurrin levels. Collectively, these findings suggest that SbGATA22 may act as a negative regulator of SbCYP79A1 expression and provide a preliminary insight into the molecular regulation of dhurrin biosynthesis in sorghum.