Function analysis and stress-mediated cis-element identification in the promoter region of VqMYB15

Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae

Rafflesiaceae is a family of endangered plants whose members are solely parasitic to the tropical grape vine Tetrastigma (Vitaceae). Currently, the genetics of their crosstalk with the host remains unexplored. In this study, we use homology-based in silico approaches to characterize micro-RNAs (miRNAs) expressed by Sapria himalayana and Rafflesia cantleyi from published omics data. Derived from secondary structures or hairpins, miRNAs are small regulators of gene expression. We found that some plant-conserved miRNA still exists in Rafflesiaceae. Out of 9 highly conserved miRNA families in plants, 7 families (156/157, 159/319, 160, 165/166, 171, 172, 390) were identified with a total of 22 variants across Rafflesiaceae. Some miRNAs were missing endogenous targets and may have evolved to target host miRNA, though this requires experimental verification. Rafflesiaceae miRNA promoters are mostly inducible by ethylene that mediates stress response in the host but could be perceived by the parasites as a signal for growth. This study provides evidence that certain miRNAs with ancient origins in land plants still exist in Rafflesiaceae, though some may have been coopted by parasites to target host genes.

Expression divergence of BAG gene family in maize under heat stress

Heat stress poses a significant challenge for maize production, especially during the spring when high temperatures disrupt cellular processes, impeding plant growth and development. The B-cell lymphoma-2 (Bcl-2) associated athanogene (BAG) gene family is known to be relatively conserved across various species. It plays a crucial role as molecular chaperone cofactors that are responsible for programmed cell death and tumorigenesis. Once the plant is under heat stress, the BAG genes act as co-chaperones and modulate the molecular functions of HSP70/HSC70 saving the plant from the damage of high temperature stress. The study was planned to identify and characterize the BAG genes for heat stress responsiveness in maize. Twenty-one (21) BAG genes were identified in the latest maize genome. The evolutionary relationship of Zea mays BAGs (ZmBAGs) with Arabidopsis thaliana, Solanum lycopersicum, Theobroma cacao, Sorghum bicolor, Ananas comosus, Physcomitrium patens, Oryza sativa and Populus trichocarpa were represented by the phylogenetic analysis. Differential expressions of BAG gene family in leaf, endosperm, anther, silk, seed and developing embryo depict their contribution to the growth and development. The in-silico gene expression analysis indicated ZmBAG-8 (Zm00001eb170080), and ZmBAG-11 (Zm00001eb237960) showed higher expression under abiotic stresses (cold, heat and salinity). The RT-qPCR further confirmed the expression of ZmBAG-8 and ZmBAG-11 in plant leaf tissue across the contrasting inbred lines and their F1 hybrid (DR-139, UML-1 and DR-139 × UML-1) when exposed to heat stress. Furthermore, the protein-protein interaction networks of ZmBAG-8 and ZmBAG-11 further elucidated their role in stress tolerance related pathways. This research offers a roadmap to plan functional research and utilize ZmBAG genes to enhance heat tolerance in grasses.

Artificially designed synthetic promoter for a high level of salt induction using a cis-engineering approach

This work aimed to design a synthetic salt-inducible promoter using a cis-engineering approach. The designed promoter (PS) comprises a minimal promoter sequence for basal-level expression and upstream cis-regulatory elements (CREs) from promoters of salinity-stress-induced genes. The copy number, spacer lengths, and locations of CREs were manually determined based on their occurrence within native promoters. The initial activity profile of the synthesized PS promoter in transiently transformed N. tabacum leaves shows a seven-fold, five-fold, and four-fold increase in reporter GUS activity under salt, drought, and abscisic acid stress, respectively, at the 24-h interval, compared to the constitutive CaMV35S promoter. Analysis of gus expression in stable Arabidopsis transformants showed that the PS promoter induces over a two-fold increase in expression under drought or abscisic acid stress and a five-fold increase under salt stress at 24- and 48-h intervals, compared to the CaMV35S promoter. The promoter PS exhibits higher and more sustained activity under salt, drought, and abscisic acid stress compared to the constitutive CaMV35S.

Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits

BACKGROUND

Phospholipases constitute a diverse category of enzymes responsible for the breakdown of phospholipids. Their involvement in signal transduction with a pivotal role in plant development and stress responses is well documented.

RESULTS

In the present investigation, a thorough genome-wide analysis revealed that the pearl millet genome contains at least 44 phospholipase genes distributed across its 7 chromosomes, with chromosome one harbouring the highest number of these genes. The synteny analysis suggested a close genetic relationship of pearl millet phospholipases with that of foxtail millet and sorghum. All identified genes were examined to unravel their gene structures, protein attributes, cis-regulatory elements, and expression patterns in two pearl millet genotypes contrasting for rancidity. All the phospholipases have a high alpha-helix content and distorted regions within the predicted secondary structures. Moreover, many of these enzymes possess binding sites for both metal and non-metal ligands. Additionally, the putative promoter regions associated with these genes exhibit multiple copies of cis-elements specifically responsive to biotic and abiotic stress factors and signaling molecules. The transcriptional profiling of 44 phospholipase genes in two genotypes contrasting for rancidity across six key tissues during pearl millet growth revealed a predominant expression in grains, followed by seed coat and endosperm. Specifically, the genes PgPLD-alpha1-1, PgPLD-alpha1-5, PgPLD-delta1-7a, PgPLA1-II-1a, and PgPLD-delta1-2a exhibited notable expression in grains of both the genotypes while showing negligible expression in the other five tissues. The sequence alignment of putative promoters revealed several variations including SNPs and InDels. These variations resulted in modifications to the corresponding cis-acting elements, forming distinct transcription factor binding sites suggesting the transcriptional-level regulation for these five genes in pearl millet.

CONCLUSIONS

The current study utilized a genome-wide computational analysis to characterize the phospholipase gene family in pearl millet. A comprehensive expression profile of 44 phospholipases led to the identification of five grain-specific candidates. This underscores a potential role for at least these five genes in grain quality traits including the regulation of rancidity in pearl millet. Therefore, this study marks the first exploration highlighting the possible impact of phospholipases towards enhancing agronomic traits in pearl millet.

Genome-wide identification and characterization of DTX family genes highlighting their locations, functions, and regulatory factors in banana (Musa acuminata)

The detoxification efflux carriers (DTX) are a significant group of multidrug efflux transporter family members that play diverse functions in all kingdoms of living organisms. However, genome-wide identification and characterization of DTX family transporters have not yet been performed in banana, despite its importance as an economic fruit plant. Therefore, a detailed genome-wide analysis of DTX family transporters in banana (Musa acuminata) was conducted using integrated bioinformatics and systems biology approaches. In this study, a total of 37 DTX transporters were identified in the banana genome and divided into four groups (I, II, III, and IV) based on phylogenetic analysis. The gene structures, as well as their proteins' domains and motifs, were found to be significantly conserved. Gene ontology (GO) annotation revealed that the predicted DTX genes might play a vital role in protecting cells and membrane-bound organelles through detoxification mechanisms and the removal of drug molecules from banana cells. Gene regulatory analyses identified key transcription factors (TFs), cis-acting elements, and post-transcriptional regulators (miRNAs) of DTX genes, suggesting their potential roles in banana. Furthermore, the changes in gene expression levels due to pathogenic infections and non-living factor indicate that banana DTX genes play a role in responses to both biotic and abiotic stresses. The results of this study could serve as valuable tools to improve banana quality by protecting them from a range of environmental stresses.

The Arabidopsis Mitochondrial Nucleoid-Associated Protein WHIRLY2 Is Required for a Proper Response to Salt Stress

In the last years, plant organelles have emerged as central coordinators of responses to internal and external stimuli, which can induce stress. Mitochondria play a fundamental role as stress sensors being part of a complex communication network between the organelles and the nucleus. Among the different environmental stresses, salt stress poses a significant challenge and requires efficient signaling and protective mechanisms. By using the why2 T-DNA insertion mutant and a novel knock-out mutant prepared by CRISPR/Cas9-mediated genome editing, this study revealed that WHIRLY2 is crucial for protecting mitochondrial DNA (mtDNA) integrity during salt stress. Loss-of-function mutants show an enhanced sensitivity to salt stress. The disruption of WHIRLY2 causes the impairment of mtDNA repair that results in the accumulation of aberrant recombination products, coinciding with severe alterations in nucleoid integrity and overall mitochondria morphology besides a compromised redox-dependent response and misregulation of antioxidant enzymes. The results of this study revealed that WHIRLY2-mediated structural features in mitochondria (nucleoid compactness and cristae) are important for an effective response to salt stress.

Genome‑wide identification and expression analysis of the UBC gene family in wheat (Triticum aestivum L.)

BACKGROUND

Ubiquitination is an important regulatory step of selective protein degradation in the plant UPS (ubiquitin-proteasome system), which is involved in various biological processes in eukaryotes. Ubiquitin-conjugating enzymes play an intermediate role in the process of protein ubiquitination reactions and thus play an essential role in regulating plant growth and response to adverse environmental conditions. However, a genome-wide analysis of the UBC gene family in wheat (Triticum aestivum L.) has not yet been performed.

RESULTS

In this study, the number, physiochemical properties, gene structure, collinearity, and phylogenetic relationships of TaUBC family members in wheat were analyzed using bioinformatics methods. The expression pattern of TaUBC genes in different tissues/organs and developmental periods, as well as the transcript levels under abiotic stress treatment, were analyzed using RNA-Seq data and qRT-PCR. Meanwhile, favorable haplotypes of TaUBC25 were investigated based on wheat resequencing data of 681 wheat cultivars from the Wheat Union Database. The analyses identified a total of 93 TaUBC family members containing a UBC domain in wheat genome. These genes were unevenly distributed across 21 chromosomes, and numerous duplication events were observed between gene members. Based on phylogenetic analysis, the TaUBC family was divided into 13 E2 groups and a separate UEV group. We investigated the expression of TaUBC family genes under different tissue/organ and stress conditions by quantitative real-time PCR (qRT-PCR) analysis. The results showed that some TaUBC genes were specifically expressed in certain tissues/organs and that most TaUBC genes responded to NaCl, PEG6000, and ABA treatment with different levels of expression. In addition, we performed association analysis for the two haplotypes based on key agronomic traits such as thousand-kernel weight (TKW), kernel length (KL), kernel weight (KW), and kernel thickness (KT), examining 122 wheat accessions at three environmental sites. The results showed that TaUBC25-Hap II had significantly higher TKW, KL, KW, and KT than TaUBC25-Hap I. The distribution analysis of haplotypes showed that TaUBC25-Hap II was preferred in the natural population of wheat.

CONCLUSION

Our results identified 93 members of the TaUBC family in wheat, and several genes involved in grain development and abiotic stress response. Based on the SNPs detected in the TaUBC sequence, two haplotypes, TaUBC25-Hap I and TaUBC25-Hap II, were identified among wheat cultivars, and their potential value for wheat breeding was validated by association analysis. The above results provide a theoretical basis for elucidating the evolutionary relationships of the TaUBC gene family and lay the foundation for studying the functions of family members in the future.

Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera)

BACKGROUND

Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm.

RESULTS

We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses.

CONCLUSION

The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.

Genome wide identification and characterization of the amino acid transporter (AAT) genes regulating seed protein content in chickpea (Cicer arietinum L.)

Amino acid transporters (AATs), besides, being a crucial component for nutrient partitioning system are also vital for growth and development of the plants and stress resilience. In order to understand the role of AAT genes in seed quality proteins, a comprehensive analysis of AAT gene family was carried out in chickpea leading to identification of 109 AAT genes, representing 10 subfamilies with random distribution across the chickpea genome. Several important stress responsive cis-regulatory elements like Myb, ABRE, ERE were detected in the promoter region of these CaAAT genes. Most of the genes belonging to the same sub-families shared the intron-exon distribution pattern owing to their conserved nature. Random distribution of these CaAAT genes was observed on plasma membrane, vacuolar membrane, Endoplasmic reticulum and Golgi membranes, which may be associated to distinct biochemical pathways. In total 92 out 109 CaAAT genes arise as result of duplication, among which segmental duplication was more prominent over tandem duplication. As expected, the phylogenetic tree was divided into 2 major clades, and further sub-divided into different sub-families. Among the 109 CaAAT genes, 25 were found to be interacting with 25 miRNAs, many miRNAs like miR156, miR159 and miR164 were interacting only with single AAT genes. Tissues specific expression pattern of many CaAAT genes was observed like CaAAP7 and CaAVT18 in nodules, CaAAP17, CaAVT5 and CaCAT9 in vegetative tissues while CaCAT10 and CaAAP23 in seed related tissues as per the expression analysis. Mature seed transcriptome data revealed that genotypes having high protein content (ICC 8397, ICC 13461) showed low CaAATs expression as compared to the genotypes having low protein content (FG 212, BG 3054). Amino acid profiling of these genotypes revealed a significant difference in amount of essential and non-essential amino acids, probably due to differential expression of CaAATs. Thus, the present study provides insights into the biological role of AAT genes in chickpea, which will facilitate their functional characterization and role in various developmental stages, stress responses and involvement in nutritional quality enhancement.

Genome-Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea (Vigna unguiculata (L.) Walp.)

In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for the synthesis of their associated factors like domain, small RNAs (sRNAs), transcription factors, micro-RNAs, and cis-acting factors that shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, subcellular locations, gene ontology (GO) terms, and regulatory factors (transcription factors, micro-RNAs, and cis-acting elements (CAEs)) to characterize the VuRNAi genes and proteins in cowpea in response to stresses. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10, and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages, and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted CAEs from the VuRNAi genes might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their associated components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress. The manuscript is available as a preprint at this link: doi:10.1101/2023.02.15.528631v1.

Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius

The basic helix-loop-helix (bHLH) transcription factors possess DNA-binding and dimerization domains and are involved in various biological and physiological processes, such as growth and development, the regulation of secondary metabolites, and stress response. However, the bHLH gene family in C. tinctorius has not been investigated. In this study, we performed a genome-wide identification and analysis of bHLH transcription factors in C. tinctorius. A total of 120 CtbHLH genes were identified, distributed across all 12 chromosomes, and classified into 24 subfamilies based on their phylogenetic relationships. Moreover, the 120 CtbHLH genes were subjected to comprehensive analyses, including protein sequence alignment, evolutionary assessment, motif prediction, and the analysis of promoter cis-acting elements. The promoter region analysis revealed that CtbHLH genes encompass cis-acting elements and were associated with various aspects of plant growth and development, responses to phytohormones, as well as responses to both abiotic and biotic stresses. Expression profiles, sourced from transcriptome databases, indicated distinct expression patterns among these CtbHLH genes, which appeared to be either tissue-specific or specific to certain cultivars. To further explore their functionality, we determined the expression levels of fifteen CtbHLH genes known to harbor motifs related to abiotic and hormone responses. This investigation encompassed treatments with ABA, salt, drought, and MeJA. The results demonstrated substantial variations in the expression patterns of CtbHLH genes in response to these abiotic and hormonal treatments. In summary, our study establishes a solid foundation for future inquiries into the roles and regulatory mechanisms of the CtbHLH gene family.

OsBTBZ1 Confers Salt Stress Tolerance in Arabidopsis thaliana

Rice (Oryza sativa L.), one of the most important commodities and a primary food source worldwide, can be affected by adverse environmental factors. The chromosome segment substitution line 16 (CSSL16) of rice is considered salt-tolerant. A comparison of the transcriptomic data of the CSSL16 line under normal and salt stress conditions revealed 511 differentially expressed sequence (DEseq) genes at the seedling stage, 520 DEseq genes in the secondary leaves, and 584 DEseq genes in the flag leaves at the booting stage. Four BTB genes, OsBTBZ1, OsBTBZ2, OsBTBN3, and OsBTBN7, were differentially expressed under salt stress. Interestingly, only OsBTBZ1 was differentially expressed at the seedling stage, whereas the other genes were differentially expressed at the booting stage. Based on the STRING database, OsBTBZ1 was more closely associated with other abiotic stress-related proteins than other BTB genes. The highest expression of OsBTBZ1 was observed in the sheaths of young leaves. The OsBTBZ1-GFP fusion protein was localized to the nucleus, supporting the hypothesis of a transcriptionally regulatory role for this protein. The bt3 Arabidopsis mutant line exhibited susceptibility to NaCl and abscisic acid (ABA) but not to mannitol. NaCl and ABA decreased the germination rate and growth of the mutant lines. Moreover, the ectopic expression of OsBTBZ1 rescued the phenotypes of the bt3 mutant line and enhanced the growth of wild-type Arabidopsis under stress conditions. These results suggest that OsBTBZ1 is a salt-tolerant gene functioning in ABA-dependent pathways.

Genome-wide identification and expression of monoacylglycerol lipase (MAGL) gene family in peanut (Arachis hypogaea L.) and functional analysis of AhMGATs in neutral lipid metabolism

Monoacylglycerol lipase (MAGL) involved in regulating plant growth and development and stress responses, hydrolyzes monoacylglycerol (MAG) into free fatty acid and glycerol, which is the last step of triacylglycerol (TAG) breakdown. Here, a genome-wide characterization of MAGL gene family from cultivated peanut (Arachis hypogaea L.) was performed. In total, 24 MAGL genes were identified and unevenly distributed on 14 chromosomes, encoding 229-414 amino acids with molecular weights ranging from 25.91 to 47.01 kDa. Spatiotemporal and stress-induced expression was analyzed by qRT-PCR. Multiple sequence alignment revealed that AhMAGL1a/b and AhMAGL3a/b were the only four bifunctional enzymes with conserved regions of hydrolase and acyltransferase, which could also be named as AhMGATs. GUS histochemical assay showed that AhMAGL1a and -1b were strongly expressed in all tissues of the plants; whereas both AhMAGL3a and -3b were weakly expressed in plants. Subcellular localization analysis indicated that AhMGATs were localized in the endoplasmic reticulum and/or Golgi complex. Seed-specific overexpression of AhMGATs in Arabidopsis decreased the oil content of the seeds and altered the fatty acid compositions, indicating that AhMGATs were involved in TAG breakdown but not TAG biosynthesis in plant seeds. This study lays the foundation for better understanding AhMAGL genes biological function in planta.

VvPL15 Is the Core Member of the Pectate Lyase Gene Family Involved in Grape Berries Ripening and Softening

The process of ripening and softening in grape begins at veraison and is closely related to the depolymerization of pectin components. A variety of enzymes are involved in pectin metabolism and one class of enzyme, pectin lyases (PLs), have been reported to play an important role in softening in many fruits; however, little information is available on the VvPL gene family in grape. In this study, 16 VvPL genes were identified in the grape genome using bioinformatics methods. Among them, VvPL5, VvPL9, and VvPL15 had the highest expression levels during grape ripening, which suggests that these genes are involved in grape ripening and softening. Furthermore, overexpression of VvPL15 affects the contents of water-soluble pectin (WSP) and acid-soluble pectin (ASP) in the leaves of Arabidopsis and significantly changes the growth of Arabidopsis plants. The relationship between VvPL15 and pectin content was further determined by antisense expression of VvPL15. In addition, we also studied the effect of VvPL15 on fruit in transgenic tomato plants, which showed that VvPL15 accelerated fruit ripening and softening. Our results indicate that VvPL15 plays an important role in grape berry softening during ripening by depolymerizing pectin.

Genome-wide identification of the TIFY family reveals JAZ subfamily function in response to hormone treatment in Betula platyphylla

BACKGROUND

The TIFY family is a plant-specific gene family and plays an important role in plant growth and development. But few reports have been reported on the phylogenetic analysis and gene expression profiling of TIFY family genes in birch (Betula platyphylla).

RESULTS

In this study, we characterized TIFY family and identified 12 TIFY genes and using phylogeny and chromosome mapping analysis in birch. TIFY family members were divided into JAZ, ZML, PPD and TIFY subfamilies. Phylogenetic analysis revealed that 12 TIFY genes were clustered into six evolutionary branches. The chromosome distribution showed that 12 TIFY genes were unevenly distributed on 5 chromosomes. Some TIFY family members were derived from gene duplication in birch. We found that six JAZ genes from JAZ subfamily played essential roles in response to Methyl jasmonate (MeJA), the JAZ genes were correlated with COI1 under MeJA. Co-expression and GO enrichment analysis further revealed that JAZ genes were related to hormone. JAZ proteins involved in the ABA and SA pathways. Subcellular localization experiments confirmed that the JAZ proteins were localized in the nucleus. Yeast two-hybrid assay showed that the JAZ proteins may form homologous or heterodimers to regulate hormones.

CONCLUSION

Our results provided novel insights into biological function of TIFY family and JAZ subfamily in birch. It provides the theoretical reference for in-depth analysis of plant hormone and molecular breeding design for resistance.

Promoter Cis-Element Analyses Reveal the Function of αVPE in Drought Stress Response of Arabidopsis

Vacuolar processing enzyme (VPE) is a cysteine protease responsible for vacuolar proteins’ maturation and regulation of programmed cell death (PCD). Four isoforms of Arabidopsis thaliana VPEs were identified previously, but only the functions of βVPE, γVPE, and δVPE were determined. The specific function of a gene is linked to the cis-acting elements in the promoter region. A promoter analysis found repetitive drought-related cis-elements in αVPE, which highlight its potential involvement in drought regulation in A. thaliana. The further co-expression network portraying genes interacting with αVPE substantiated its drought-regulation-related function. Expression of αVPE was upregulated after drought treatment in A. thaliana. To confirm the role of αVPE, a loss of function study revealed that αVPE knockout mutants remained green compared with WT after drought treatment. The mutants had reduced proline activity, decreased sucrose content, and lower MDA content, but increased photosynthetic pigments, indicating that αVPE negatively regulates drought tolerance in A. thaliana. Taken together, our findings serve as important evidence of the involvement of αVPE in modulating drought tolerance in A. thaliana.

Genome wide identification of GDSL gene family explores a novel GhirGDSL26 gene enhancing drought stress tolerance in cotton

BACKGROUND

Current climate change scenarios are posing greater threats to the growth and development of plants. Thus, significant efforts are required that can mitigate the negative effects of drought on the cotton plant. GDSL esterase/lipases can offer an imperative role in plant development and stress tolerance. However, thesystematic and functional roles of the GDSL gene family, particularly in cotton under water deficit conditions have not yet been explored.

RESULTS

In this study, 103, 103, 99, 198, 203, 239, 249, and 215 GDSL proteins were identified in eight cotton genomes i.e., Gossypium herbaceum (A1), Gossypium arboretum (A2), Gossypium raimondii (D5), Gossypium hirsutum (AD1), Gossypium barbadense (AD2), Gossypium tomentosum (AD3), Gossypium mustelinum (AD4), Gossypium darwinii (AD5), respectively. A total of 198 GDSL genes of Gossypium hirsutum were divided into eleven clades using phylogenetic analysis, and the number of GhirGDSL varied among different clades. The cis-elements analysis showed that GhirGDSL gene expression was mainly related to light, plant hormones, and variable tense environments. Combining the results of transcriptome and RT-qPCR, GhirGDSL26 (Gh_A01G1774), a highly up-regulated gene, was selected for further elucidating its tole in drought stress tolerance via estimating physiological and biochemical parameters. Heterologous expression of the GhirGDSL26 gene in Arabidopsis thaliana resulted in a higher germination and survival rates, longer root lengths, lower ion leakage and induced stress-responsive genes expression under drought stress. This further highlighted that overexpressed plants had a better drought tolerance as compared to the wildtype plants. Moreover, 3, 3'-diaminobenzidine (DAB) and Trypan staining results indicated reduced oxidative damage, less cell membrane damage, and lower ion leakage in overexpressed plants as compared to wild type. Silencing of GhirGDSL26 in cotton via VIGS resulting in a susceptible phenotype, higher MDA and H₂O₂ contents, lower SOD activity, and proline content.

CONCLUSION

Our results demonstrated that GhirGDSL26 plays a critical role in cotton drought stress tolerance. Current findings enrich our knowledge of GDSL genes in cotton and provide theoretical guidance and excellent gene resources for improving drought tolerance in cotton.

Conserved and divergent evolution of the bZIP transcription factor in five diploid Gossypium species

495 bZIP members with 12 subfamilies were identified in the five diploid cottons. Segmental duplication events in cotton ancestor might have led to primary expansion of the cotton bZIP members. The basic leucine zipper (bZIP) transcription factor is one of the largest and most diverse families in plants. The evolutionary history of the bZIP family is still unclear in cotton. In this study, a total of 495 bZIP members were identified in five diploid Gossypium species, including 100 members in Gossypium arboreum, 104 members in Gossypium herbaceum, 95 members in Gossypium raimondii, 96 members in Gossypium longicalyx, and 100 members in Gossypium turneri. The bZIP members could be divided into 12 subfamilies with biased gene proportions, gene structures, conserved motifs, expansion rates, gene loss rates, and cis-regulatory elements. A total of 239 duplication events were identified in the five Gossypium species, and mainly occurred in their common ancestor. Furthermore, some GabZIPs and GhebZIPs could be regarded as important candidates in cotton breeding. The bZIP members had a conserved and divergent evolution in the five diploid Gossypium species. The current study laid an important foundation on the evolutionary history of the bZIP family in cotton.

Genome-wide identification and functional analysis of Dof transcription factor family in Camelina sativa

BACKGROUND

Dof transcription factors (TFs) containing C₂-C₂ zinc finger domains are plant-specific regulatory proteins, playing crucial roles in a variety of biological processes. However, little is known about Dof in Camelina sativa, an important oil crop worldwide, with high stress tolerance. In this study, a genome-wide characterization of Dof proteins is performed to examine their basic structural characteristics, phylogenetics, expression patterns, and functions to identify the regulatory mechanism underlying lipid/oil accumulation and the candidate Dofs mediating stress resistance regulation in C. sativa.

RESULTS

Total of 103 CsDof genes unevenly distributed on 20 chromosomes were identified from the C. sativa genome, and they were classified into four groups (A, B, C and D) based on the classification of Arabidopsis Dof gene family. All of the CsDof proteins contained the highly-conserved typic CX₂C-X₂₁-CX₂C structure. Segmental duplication and purifying selection were detected for CsDof genes. 61 CsDof genes were expressed in multiple tissues, and 20 of them showed tissue-specific expression patterns, suggesting that CsDof genes functioned differentially in different tissues of C. sativa. Remarkably, a set of CsDof members were detected to be possible involved in regulation of oil/lipid biosynthesis in C. sativa. Six CsDof genes exhibited significant expression changes in seedlings under salt stress treatment.

CONCLUSIONS

The present data reveals that segmental duplication is the key force responsible for the expansion of CsDof gene family, and a strong purifying pressure plays a crucial role in CsDofs' evolution. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Several CsDof TFs may mediate lipid metabolism and stress responses in C. sativa. Collectively, our findings provide a foundation for deep understanding the roles of CsDofs and genetic improvements of oil yield and salt stress tolerance in this species and the related crops.

Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development

Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.

Genome-wide identification of HD-ZIP transcription factors in maize and their regulatory roles in promoting drought tolerance

Drought is the main limiting factor of maize productivity, therefore improving drought tolerance in maize has potential practical importance. Cloning and functional verification of drought-tolerant genes is of great importance to understand molecular mechanisms under drought stress. Here, we employed a bioinformatic pipeline to identify 42 ZmHDZ drought responsive genes using previously reported maize transcriptomic datasets. The coding sequences, exon-intron structure and domain organization of all the 42 genes were identified. Phylogenetic analysis revealed evolutionary conservation of members of the ZmHDZ genes in maize. Several regulatory elements associated with drought tolerance were identified in the promoter regions of ZmHDZ genes, indicating the implication of these genes in plant response to drought stress. 42 ZmHDZ genes were distributed unevenly on 10 chromosomes, and 24 pairs of gene duplications were the segmental duplication. The expression of several ZmHDZ genes was upregulated under drought stress, and ZmHDZ9 overexpressing transgenic plants exhibited higher SOD and POD activities and higher accumulation of soluble proteins under drought stress which resulted in enhanced developed phenotype and improved resistance. The present study provides evidence for the evolutionary conservation of HD-ZIP transcription factors homologs in maize. The results further provide a comprehensive insight into the roles of ZmHDZ genes in regulating drought stress tolerance in maize.

Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum

Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.

Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.)

Calmodulin (CaM) is considered as the most significant Ca²⁺ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.

Genome-wide identification, characterization and expression analysis of the LIM transcription factor family in quinoa

Lim family members play an important role in the regulation of plant cell development and stress response. However, there are few studies on LIM family in quinoa. In this study, we identified nine LIMS (named cqlim01-cqlim09) from quinoa, which were divided into three subfamilies (α Lim1, γ lim2 and δ lim2) according to phylogeny. The differences in gene structure and motif composition among different subfamilies have been observed. In addition, we studied the repetitive events of the members of the family. The Ka/Ks (non synchronous substitution rate / synchronous substitution rate) ratio analysis showed that the repetitive CqLIMs probably experienced purifying selection pressure. Promoter analysis showed that the family genes contained a variety of hormones, stress and tissue-specific expression elements, and protein interactions showed that these genes had actin stabilizing effect. In addition, QRT PCR results showed that all CqLIM genes were positively regulated under three stresses (low temperature, salt and ABA). These results provide a theoretical basis of further study of LIM gene in quinoa.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00988-2.