Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa

Genome-Wide Comparative Analysis of Five Amaranthaceae Species Reveals a Large Amount of Repeat Content

Amaranthus is a genus of C4 dicotyledonous herbaceous plant species that are widely distributed in Asia, Africa, Australia, and Europe and are used as grain, vegetables, forages, and ornamental plants. Amaranth species have gained significant attention nowadays as potential sources of nutritious food and industrial products. In this study, we performed a comparative genome analysis of five amaranth species, namely, Amaranthus hypochondriacus, Amaranthus tuberculatus, Amaranthus hybridus, Amaranthus palmeri, and Amaranthus cruentus. The estimated repeat content ranged from 54.49% to 63.26% and was not correlated with the genome sizes. Out of the predicted repeat classes, the majority of repetitive sequences were Long Terminal Repeat (LTR) elements, which account for about 13.91% to 24.89% of all amaranth genomes. Phylogenetic analysis based on 406 single-copy orthologous genes revealed that A. hypochondriacus is most closely linked to A. hybridus and distantly related to A. cruentus. However, dioecious amaranth species, such as A. tuberculatus and A. palmeri, which belong to the subgenera Amaranthus Acnida, have formed their distinct clade. The comparative analysis of genomic data of amaranth species will be useful to identify and characterize agronomically important genes and their mechanisms of action. This will facilitate genomics-based, evolutionary studies, and breeding strategies to design faster, more precise, and predictable crop improvement programs.

Genome-wide analysis of bZIP gene family members in Pleurotus ostreatus, and potential roles of PobZIP3 in development and the heat stress response

The basic leucine zipper (bZIP) transcription factor (TF) is widespread among eukaryotes and serves different roles in fungal processes including nutrient utilization, growth, stress responses and development. The oyster mushroom (Pleurotus ostreatus) is an important and widely cultivated edible mushroom worldwide; nevertheless, reports are lacking on the identification or function of bZIP gene family members in P. ostreatus. Herein, 11 bZIPs on 6 P. ostreatus chromosomes were systematically identified, which were classified into 3 types according to their protein sequences. Phylogenetic analysis of PobZIPs with other fungal bZIPs indicated that PobZIPs may have differentiated late. Cis-regulatory element analysis revealed that at least one type of stress-response-related element was present on each bZIP promoter. RNA-seq and RT-qPCR analyses revealed that bZIP expression patterns were altered under heat stress and different developmental stages. We combined results from GST-Pull-down, EMSA and yeast two-hybrid assays to screen a key heat stress-responsive candidate gene PobZIP3. PobZIP3 overexpression in P. ostreatus enhanced tolerance to high temperature and cultivation assays revealed that PobZIP3 positively regulates the development of P. ostreatus. RNA-seq analysis showed that PobZIP3 plays a role in glucose metabolism pathways, antioxidant enzyme activity and sexual reproduction. These results may support future functional studies of oyster mushroom bZIP TFs.

Genome-wide analysis of AP2/ERF gene and functional analysis of CqERF24 gene in drought stress in quinoa

Quinoa is a crop with high nutritional value and strong stress resistance. AP2/ERF transcription factors play a key role in plant growth and development. In this study, 148 AP2/ERF genes were identified in quinoa, which were divided into 5 subfamilies, including ERF, AP2, DREB, RAV and Soloist. The results showed that the number of introns ranged from 0 to 11, and the Motif 1-Motif 4 was highly conserved in most CqAP2/ERF proteins. The 148 CqAP2/ERF genes were distributed on 19 chromosomes. There were 93 pairs of duplicating genes in this family, and gene duplication played a critical role in the expansion of this family. Protein-protein interaction indicated that the proteins in CqAP2/ERF subfamily exhibited complex interactions, and GO enrichment analysis indicated that 148 CqAP2/ERF proteins were involved in transcription factor activity. In addition, CqAP2/ERF gene contains a large number of elements related to hormones in promoter region (IAA, GA, SA, ABA and MeJA) and stresses (salt, drought, low temperature and anaerobic induction). Transcriptome analysis under drought stress indicated that most of the CqAP2/ERF genes were responsive to drought stress, and subcellular localization indicated that CqERF24 was location in the nucleus, qRT-PCR results also showed that most of the genes such as CqERF15, CqERF24, CqDREB03, CqDREB14, CqDREB37 and CqDREB43 also responded to drought stress in roots and leaves. Overexpression of CqERF24 in Arabidopsis thaliana enhanced drought resistance by increasing antioxidant enzyme activity and activation-related stress genes, and the gene is sensitive to ABA, while silencing CqERF24 in quinoa decreased drought tolerance. In addition, overexpression of CqERF24 in quinoa calli enhanced resistance to mannitol. These results lay a solid foundation for further study on the role of AP2/ERF family genes in quinoa under drought stress.

The Association between BZIP Transcription Factors and Flower Development in Litsea cubeba

The basic leucine zipper (bZIP) family is one of the largest families of transcription factors among eukaryotic organisms. Members of the bZIP family play various roles in regulating the intricate process of flower development in plants. Litsea cubeba (Lour.) (family: Lauraceae) is an aromatic, dioecious plant used in China for a wide range of applications. However, no study to date has undertaken a comprehensive analysis of the bZIP gene family in L. cubeba. In this work, we identified 68 members of the bZIP gene family in L. cubeba and classified them into 12 subfamilies based on previous studies on Arabidopsis thaliana. Transcriptome data analysis revealed that multiple LcbZIP genes exhibit significantly high expression levels in the flowers of L. cubeba, while some also demonstrate distinct temporal specificity during L. cubeba flower development. In particular, some LcbZIP genes displayed specific and high expression levels during the stamen and pistil degradation process. Using differential gene expression analysis, weighted gene co-expression network analysis, and Gene Ontology enrichment analysis, we identified six candidate LcbZIP genes that potentially regulate stamen or pistil degradation during flower development. In summary, our findings provide a framework for future functional analysis of the LcbZIP gene family in L. cubeba and offer novel insights for investigating the mechanism underlying pistil and stamen degeneration in this plant.

Molecular Characterization and Expression Analysis of YABBY Genes in Chenopodium quinoa

Plant-specific YABBY transcription factors play an important role in lateral organ development and abiotic stress responses. However, the functions of the YABBY genes in quinoa remain elusive. In this study, twelve YABBY (CqYAB) genes were identified in the quinoa genome, and they were distributed on nine chromosomes. They were classified into FIL/YAB3, YAB2, YAB5, INO, and CRC clades. All CqYAB genes consist of six or seven exons, and their proteins contain both N-terminal C2C2 zinc finger motifs and C-terminal YABBY domains. Ninety-three cis-regulatory elements were revealed in CqYAB gene promoters, and they were divided into six groups, such as cis-elements involved in light response, hormone response, development, and stress response. Six CqYAB genes were significantly upregulated by salt stress, while one was downregulated. Nine CqYAB genes were upregulated under drought stress, whereas six CqYAB genes were downregulated under cadmium treatment. Tissue expression profiles showed that nine CqYAB genes were expressed in seedlings, leaves, and flowers, seven in seeds, and two specifically in flowers, but no CqYAB expression was detected in roots. Furthermore, CqYAB4 could rescue the ino mutant phenotype in Arabidopsis but not CqYAB10, a paralog of CqYAB4, indicative of functional conservation and divergence among these YABBY genes. Taken together, these results lay a foundation for further functional analysis of CqYAB genes in quinoa growth, development, and abiotic stress responses.

Comprehensive Functional Analysis of the bZIP Family in Bletilla striata Reveals That BsbZIP13 Could Respond to Multiple Abiotic Stresses

Basic leucine zipper (bZIP) transcription factors (TFs) are one of the largest families involved in plant physiological processes such as biotic and abiotic responses, growth, and development, etc. In this study, 66 members of the bZIP family were identified in Bletilla striata, which were divided into 10 groups based on their phylogenetic relationships with AtbZIPs. A structural analysis of BsbZIPs revealed significant intron-exon differences among BsbZIPs. A total of 63 bZIP genes were distributed across 16 chromosomes in B. striata. The tissue-specific and germination stage expression patterns of BsbZIPs were based on RNA-seq. Stress-responsive expression analysis revealed that partial BsbZIPs were highly expressed under low temperatures, wounding, oxidative stress, and GA treatments. Furthermore, subcellular localization studies indicated that BsbZIP13 was localized in the nucleus. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays suggested that BsbZIP13 could interact with multiple BsSnRK2s. The results of this study provide insightful data regarding bZIP TF as one of the stress response regulators in B. striata, while providing a theoretical basis for transgenic and functional studies of the bZIP gene family in B. striata.

Genome-wide identification of bZIP transcription factor family in Artemisia annua, its transcriptional profiling and regulatory role in phenylpropanoid metabolism under different light conditions

The basic leucine zipper (bZIP) protein transcription factors are known to modulate development, plant growth, metabolic response, and resistance to several biotic and abiotic stressors and have been widely studied in the model plant Arabidopsis thaliana. However, no comprehensive information about the bZIP transcription factor family in Artemisia annua has been explored to date. In this genome-wide study, we identified 61 bZIP TFs after removing false positives and incomplete sequences from Artemisia annua. Seven highly expressed homolog AabZIP TF genes under UV-B and differential light conditions in different tissues were identified from the publicly available microarray dataset as having their cis-regulatory elements involved in, flavonoids biosynthesis, seed-specific gene regulation, stress responses, and metabolic regulation. In-silico analysis and electrophoretic mobility shift assay (EMSA) confirmed the interaction of AabZIP19 TF over the AaPAL1 promoter in order to regulate the phenolics and flavonoid biosynthesis via the phenylpropanoid pathway. Further, RT-PCR analysis has been carried out to validate the transcript levels of selected AabZIP genes under white light, red light, blue light (45 min), and UV-B exposure (12 and 24 h). These genes have their highest expression levels under UV-B and blue light exposure, in contrast with white light. Therefore, the detection of ROS through staining confirms the accumulation of superoxide radicals and H2O2, and in addition to reducing ROS accumulation under UV-B and blue light irradiation, total phenols and flavonoids are significantly enhanced. This study laid the groundwork for deciphering the possible role of AabZIP TFs under different light stress-responsive conditions and in the regulation of secondary metabolism.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01338-0.

An Evidence Theory and Fuzzy Logic Combined Approach for the Prediction of Potential ARF-Regulated Genes in Quinoa

Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental factors. Quinoa was selected as among the model crops destined for bio-saline agriculture that could contribute to the staple food security for an ever-growing worldwide population under various climate change scenarios. The auxin response factors (ARFs) constitute the main contributors in the plant adaptation to severe environmental conditions. Thus, the determination of the ARF-binding sites represents the major step that could provide promising insights helping in plant breeding programs and improving agronomic traits. Hence, determining the ARF-binding sites is a challenging task, particularly in species with large genome sizes. In this report, we present a data fusion approach based on Dempster-Shafer evidence theory and fuzzy set theory to predict the ARF-binding sites. We then performed an "In-silico" identification of the ARF-binding sites in Chenopodium quinoa. The characterization of some known pathways implicated in the auxin signaling in other higher plants confirms our prediction reliability. Furthermore, several pathways with no or little available information about their functions were identified to play important roles in the adaptation of quinoa to environmental conditions. The predictive auxin response genes associated with the detected ARF-binding sites may certainly help to explore the biological roles of some unknown genes newly identified in quinoa.

Genome-wide identification of the TGA gene family in kiwifruit (Actinidia chinensis spp.) and revealing its roles in response to Pseudomonas syringae pv. actinidiae (Psa) infection

Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is a destructive disease of kiwifruit worldwide. Functional genes in response to Psa infection are needed, as they could be utilized to control disease. TGACG-binding transcription factor (TGA), as an essential regulator, involved in the process of plant against pathogens. However, the function of TGA regulators has not been reported in kiwifruit. It is unclear that whether TGA genes play a role in response to Psa infection. Here, we performed genome-wide screening and identified 13 TGA genes in kiwifruit. Phylogenetic analysis showed that 13 members of the AcTGA gene family could be divided into five groups. AcTGA proteins were mainly located in the nucleus, and significant differences were identified in their 3D structures. Segmental duplications promoted the expansion of the AcTGA family. Additionally, RNA-Seq and qRT-PCR revealed that four genes (AcTGA01/06/07/09) were tissue-specific and responsive to hormones at different levels. Subcellular localization showed that four proteins located in the nucleus, and among them, three (AcTGA01/06/07) had transcriptional activation activity. Lastly, transient overexpression proved that these three genes (AcTGA01/06/07) potentially played a role in the resistance to kiwifruit canker. These results provided a theoretical basis for revealing TGA involved in kiwifruit regulation against Psa.

Genome-Wide Identification and Characterization of SPL Family Genes in Chenopodium quinoa

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode a large family of plant-specific transcription factors that play important roles in plant growth, development, and stress responses. However, there is little information available on SPL genes in Chenopodiaceae. Here, 23 SPL genes were identified and characterized in the highly nutritious crop Chenopodium quinoa. Chromosome localization analysis indicated that the 23 CqSPL genes were unevenly distributed on 12 of 18 chromosomes. Two zinc finger-like structures and a nuclear location signal were present in the SBP domains of all CqSPLs, with the exception of CqSPL21/22. Phylogenetic analysis revealed that these genes were classified into eight groups (group I–VIII). The exon–intron structure and motif composition of the genes in each group were similar. Of the 23 CqSPLs, 13 were potential targets of miR156/7. In addition, 5 putative miR156-encoding loci and 13 putative miR157-encoding loci were predicted in the quinoa genome, and they were unevenly distributed on chromosome 1–4. The expression of several Cqu-MIR156/7 loci was confirmed by reverse transcription polymerase chain reaction in seedlings. Many putative cis-elements associated with light, stress, and phytohormone responses were identified in the promoter regions of CqSPLs, suggesting that CqSPL genes are likely involved in the regulation of key developmental processes and stress responses. Expression analysis revealed highly diverse expression patterns of CqSPLs among tissues. Many CqSPLs were highly expressed in leaves, flowers, and seeds, and their expression levels were low in the roots, suggesting that CqSPLs play distinct roles in the development and growth of quinoa. The expression of 13 of 23 CqSPL genes responded to salt treatment (11 up-regulated and 2 down-regulated). A total of 22 of 23 CqSPL genes responded to drought stress (21 up-regulated and 1 down-regulated). Moreover, the expression of 14 CqSPL genes was significantly altered following cadmium treatment (3 up-regulated and 11 down-regulated). CqSPL genes are thus involved in quinoa responses to salt/drought and cadmium stresses. These findings provide new insights that will aid future studies of the biological functions of CqSPLs in C. quinoa.

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

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.

Genome-wide identification and expression analysis of bZIP transcription factors in oil palm (Elaeis guineensis Jacq.) under abiotic stress

The bZIP transcription factors are well-known transcription regulators and play a key role in regulating various developmental, biological processes, and stress responses in plants. However, information on bZIP transcription factors is not yet available in oil palm, an important oil yielding crop. The present study identified the 97 bZIP transcription factor family members in oil palm genome via a genome-wide approach. Phylogenetic analysis clustered all EgbZIPs into 12 clusters with Arabidopsis and rice bZIPs. EgbZIP gene structure analysis showed a distinct variation in the intron-exon organization among all EgbZIPs. Conserved motif analysis demonstrated the occurrence of ten additional conserved motifs besides having a common bZIP domain. All the identified 97 EgbZIPs were unevenly distributed on 16 chromosomes and exhibited tandem duplication in oil palm genome. Our results aslo demonstrated that tissue-specific expression patterns of EgbZIPs based on the available transcriptome data of six different tissue of oil palm. Stress-responsive expression analysis showed that 11EgbZIP transcription factors were highly expressed under cold, salinity, drought stress conditions. Taken together, our findings will provide insightful information on bZIP transcription factors as one of the stress-responsive regulators in oil palm.

S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response

Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.

Rewilding staple crops for the lost halophytism: Toward sustainability and profitability of agricultural production systems

Abiotic stress tolerance has been weakened during the domestication of all major staple crops. Soil salinity is a major environmental constraint that impacts over half of the world population; however, given the increasing reliance on irrigation and the lack of available freshwater, agriculture in the 21st century will increasingly become saline. Therefore, global food security is critically dependent on the ability of plant breeders to create high-yielding staple crop varieties that will incorporate salinity tolerance traits and account for future climate scenarios. Previously, we have argued that the current agricultural practices and reliance on crops that exclude salt from uptake is counterproductive and environmentally unsustainable, and thus called for a need for a major shift in a breeding paradigm to incorporate some halophytic traits that were present in wild relatives but were lost in modern crops during domestication. In this review, we provide a comprehensive physiological and molecular analysis of the key traits conferring crop halophytism, such as vacuolar Na⁺ sequestration, ROS desensitization, succulence, metabolic photosynthetic switch, and salt deposition in trichomes, and discuss the strategies for incorporating them into elite germplasm, to address a pressing issue of boosting plant salinity tolerance.