Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation.

BACKGROUND: The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance. RESULTS: In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. CONCLUSIONS: This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.

Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis.

Preserving genetic diversity is pivotal for enhancing genetic improvement and facilitating adaptive responses to selection. This study focuses on identifying key genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs), while exploring the genomic evolutionary connectedness among seven Iranian horses representing five indigenous breeds: Caspian, Turkemen, DareShuri, Kurdish, and Asil. Using whole-genome resequencing, we generated 2.7 Gb of sequence data, with raw reads ranging from 1.2 Gb for Caspian horses to 0.38 Gb for Turkoman horses. Post-filtering, approximately 1.9 Gb of reads remained, with ~ 1.5 Gb successfully mapped to the horse reference genome (EquCab3.0), achieving mapping rates between 76.4% (Caspian) and 98.35% (Turkoman). We identified 2,909,816 SNPs in Caspian horses, constituting around 0.1% of the genome. Notably, 71% of these SNPs were situated in intergenic regions, while 8.5 and 6.8% were located upstream and downstream, respectively. A comparative analysis of SNPs between Iranian and non-Iranian horse breeds showed that Caspian horses had the lowest number of shared SNPs with Turkoman horses. Instead, they showed a closer genetic relationship with DareShuri, Quarter, Arabian, Standardbred, and Asil breeds. Hierarchical clustering highlighted Caspian horses as a distinct cluster, underscoring their distinctive genomic signature. Caspian horses exhibit a unique genetic profile marked by an enrichment of private mutations in neurological genes, influencing sensory perception and awareness. This distinct genetic makeup shapes mating preferences and signifies a separate evolutionary trajectory. Additionally, significant non-synonymous single nucleotide polymorphisms (nsSNPs) in reproductive genes offer intervention opportunities for managing Caspian horses. These findings reveal the population genetic structure of Iranian horse breeds, contributing to the advancement of knowledge in areas such as conservation, performance traits, climate adaptation, reproduction, and resistance to diseases in equine science.

Diversity of the ectoines biosynthesis genes in the salt tolerant Streptomyces and evidence for inductive effect of ectoines on their accumulation.

Streptomyces commonly produce ectoines as compatible solutes to prevent osmotic stresses. Fine structure of the genes producing ectoine (ectC) and hydroxyectoine (ectD) enzymes in Streptomyces rimosus C-2012 as a slightly halophilic bacterium is reported in this study. Deduced amino acid sequences of ectC and ectD genes from strain C-2012 and some other related species were compared and 72-90% and 13-81% identities were detected for ectC and ectD, respectively. High similarity of ectC between closely or distantly related Streptomyces to the strain C-2012 may indicate horizontal transfer of this gene. However, phylogenetic relationships of ectD were correlated with phylogenetic affiliation of the strains. It suggests that the ability of Streptomyces to produce hydroxyectoine has been the result of a vertical transfer event. HPLC analysis showed that strain C-2012 was able to produce ectoine and hydroxyectoine both in the presence and absence of external salinity (up to 0.45 M NaCl). Accordingly, reverse transcription quantitative PCR (RT-qPCR) showed that ectABCD operon in this strain is positively affected by salt. Also, inductive effect of the salt was increased when it was applied with 1 mM of ectoines. Transcription level of ectC was increased 2.7- and 2.9-fold in the medium supplied with salt and ectoine and salt and hydroxyectoine, respectively. The effect of salinity with or without ectoines was more on ectD transcription level than that of ectC. In S. rimosus under salt stress, ectoine and hydroxyectoine biosynthesis primarily depends on the stimulation of ectABCD operon transcription. However, drastic accumulation of ectoine and hydroxyectoine without increase in ectC and ectD transcripts was observed in the medium supplied with salt and ectoines and that suggest there might be additional posttranscriptional level of control. Increases in ratio of some intracellular free amino acids in salt stressed to unstressed conditions were observed in cells grown with ectoines. Our results suggest the possibility of a supplementary role of ectoines to improve structure and function of the cells in stressful environments as well as their important role as osmoprotectants.

Taxonomic study of a salt tolerant Streptomyces sp. strain C-2012 and the effect of salt and ectoine on lon expression level.

Streptomyces strain C-2012 is a salt tolerant biocontrol PGPR that has been isolated from Iranian soil. The main aim of current study was finding strain C-2012 taxonomic position and to find the genes which are potentially involved in salt tolerance phenotype. Strain C-2012 chemotaxonomic, morphological and molecular characteristics indicate that this strain is a member of the genus Streptomyces. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence revealed that this strain is closely related to Streptomyces rimosus JCM 4667(T). Also, DNA-DNA hybridization test estimated 74% relatedness between two strains and confirmed that C-2012 is a strain of S. rimosus. In order to find novel genes that are differentially expressed in response to the salt treatment, cDNA-AFLP was carried out. One of the selected expressed sequence tags (TDF-1) was found to be homologous to lon gene which produces a bacterial ATP-dependent proteases (proteases LA). Lon gene expression was induced following 450 mM salt (NaCl) treatment and its expression level was further (5.2-fold) increased in response to salt when ectoine was added to the medium. These results suggest that two protein protection systems including ectoine and ATP-dependent proteases synergistically are related. NaCl stress also caused an enhancement in the activity of extracellular protease.

A proteomics approach to study the molecular basis of enhanced salt tolerance in barley (Hordeum vulgare L.) conferred by the root mutualistic fungus Piriformospora indica.

Piriformospora indica is a root-interacting mutualistic fungus capable of enhancing plant growth, increasing plant resistance to a wide variety of pathogens, and improving plant stress tolerance under extreme environmental conditions. Understanding the molecular mechanisms by which P. indica can improve plant tolerance to stresses will pave the way to identifying the major mechanisms underlying plant adaptability to environmental stresses. We conducted greenhouse experiments at three different salt levels (0, 100 and 300 mM NaCl) on barley (Hordeum vulgare L.) cultivar "Pallas" inoculated with P. indica. Based on the analysis of variance, P. indica had a significant impact on the barley growth and shoot biomass under normal and salt stress conditions. P. indica modulated ion accumulation in colonized plants by increasing the foliar potassium (K(+))/sodium (Na(+)) ratio, as it is considered a reliable indicator of salt stress tolerance. P. indica induced calcium (Ca(2+)) accumulation and likely influenced the stress signal transduction. Subsequently, proteomic analysis of the barley leaf sheath using two-dimensional electrophoresis resulted in detection of 968 protein spots. Of these detected spots, the abundance of 72 protein spots changed significantly in response to salt treatment and P. indica-root colonization. Mass spectrometry analysis of responsive proteins led to the identification of 51 proteins. These proteins belonged to different functional categories including photosynthesis, cell antioxidant defense, protein translation and degradation, energy production, signal transduction and cell wall arrangement. Our results showed that P. indica induced a systemic response to salt stress by altering the physiological and proteome responses of the plant host.

Proteomic analysis of the Mexican lime tree response to "Candidatus Phytoplasma aurantifolia" infection.

"Candidatus Phytoplasma aurantifolia" is the causative agent of witches' broom disease in the Mexican lime tree (Citrus aurantifolia L.), and is responsible for major tree losses in Southern Iran and Oman. The pathogen is strictly biotrophic, and, therefore, completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. We applied a proteomics approach to analyse gene expression in Mexican limes infected with "Ca. Phytoplasma aurantifolia". Leaf samples were collected from healthy and infected plants and were analysed using 2-DE coupled with MS. Among 800 leaf proteins that were detected reproducibly in eight biological replicates of healthy and eight biological replicates of infected plants, 55 showed a significant response to the disease. MS resulted in identification of 39 regulated proteins, which included proteins that were involved in oxidative stress defence, photosynthesis, metabolism, and the stress response. Our results provide the first proteomic view of the molecular basis of the infection process and identify genes that could help inhibit the effects of the pathogen.

Molecular diversity of arbuscular mycorrhizal fungi in relation to soil chemical properties and heavy metal contamination.

Abundance and diversity of arbuscular mycorrhizal fungi (AMF) associated with dominant plant species were studied along a transect from highly lead (Pb) and zinc (Zn) polluted to non-polluted soil at the Anguran open pit mine in Iran. Using an established primer set for AMF in the internal transcribed spacer (ITS) region of rDNA, nine different AMF sequence types were distinguished after phylogenetic analyses, showing remarkable differences in their distribution patterns along the transect. With decreasing Pb and Zn concentration, the number of AMF sequence types increased, however one sequence type was only found in the highly contaminated area. Multivariate statistical analysis revealed that further factors than HM soil concentration affect the AMF community at contaminated sites. Specifically, the soils' calcium carbonate equivalent and available P proved to be of importance, which illustrates that field studies on AMF distribution should also consider important environmental factors and their possible interactions.