The plant homeodomain (PHD) finger constitutes a subgroup of transcription factors that contribute to the coordination of plant growth, morphogenesis, and adaptation to environmental stress mechanisms. In this study, we identified and functionally characterized the BrPHD58 gene from Brassica rapa. Using sequence analysis, subcellular localization of BrPHD58-GFP fusion proteins, and transgenic Arabidopsis thaliana lines ectopically expressing BrPHD58, we investigated its role in salt stress responses, including seedling phenotypes and expression of salt-responsive genes. Subcellular localization analysis indicated that BrPHD58 predominantly accumulates within the nuclear compartment. Ectopic expression of BrPHD58 in A. thaliana significantly reduced seedling survival rates and root lengths under varying concentrations of NaCl compared to wild-type (WT) plants. Under soil-grown conditions, transgenic lines overexpressing BrPHD58 exhibited markedly decreased tolerance to salt stress. Moreover, ectopic expression of BrPHD58 led to a down regulation of key salt-responsive genes, AtRD22, AtRD29A, and AtLEA14, under salt stress conditions. Collectively, all these findings indicate that BrPHD58 acts as a negative modulator of salt stress tolerance in transgenic plants. Further investigation involving the development and analysis of BrPHD58 loss-of-function mutants in B. rapa is necessary to fully elucidate its physiological role in salinity adaptation.

Integrative genomics and bioinformatics have revolutionized plant genetics by enabling high-resolution analysis of plant genomes and providing deep mechanistic insight into the molecular basis of agronomically important traits. Advances in sequencing technologies and computational tools have elucidated the genetic and molecular processes governing plant growth, stress responses, and disease resistance. This study investigates the utility of integrative genomics and bioinformatics for identifying key genes and pathways associated with critical agronomic traits, and evaluates the potential of these approaches to enhance crop breeding strategies. Whole-genome sequencing of five plant species—rice, maize, wheat, Arabidopsis, and soybean—was performed using Illumina and PacBio platforms. Bioinformatics workflows encompassing genome assembly, annotation, RNA-Seq differential expression analysis, and genome-wide association studies (GWAS) were implemented. Multi-omics integration combining transcriptomic, proteomic, and metabolomic datasets was carried out to reconstruct molecular networks and identify genetic variants associated with key traits. Results revealed several genes significantly linked to yield, disease resistance, and drought tolerance. Multi-omics integration deepened understanding of gene regulatory networks, and machine learning algorithms identified novel biomarkers for crop improvement. Genomics-assisted breeding strategies were shown to improve parental selection efficiency. Integrative genomics and bioinformatics are essential modern tools for identifying genetic markers for crop improvement and hold considerable promise for accelerating the development of stress-tolerant, food-secure crop varieties.

Earth's biodiversity is central to ecosystem health and resilience, providing essential functions and services. The Red Sea is a recognised marine biodiversity hotspot with high endemism and unique environmental conditions that support extensive but poorly resolved biodiversity. Here, we applied metagenomic analyses to sediment samples collected from coastal to deep-sea environments during the Red Sea Decade Expedition 2022 to characterise biodiversity across the web of life. From a single shotgun assay per sample, this approach simultaneously characterised the sediment microbiome, which amplicon-based surveys recover only through parallel, targeted assays, and extended detection to higher eukaryotes. Using high-throughput sequencing, we generated 12.8 billion sequences, revealing taxa covering all domains of life. Although eukaryotic sequences represented only 0.7% of the taxonomically annotated dataset, we managed to identify 679 eukaryotic families. Prokaryotic diversity was high, as expected in a basin-scale sampling coupled with high sequencing depth, with groups covering a wide functional array. Community structure analyses revealed depth-driven stratification of open-ocean benthic microbial communities and latitudinal structuring of coastal benthic eukaryotes. Overall, this dataset provides an empirical reliability-coverage trade-off with direct consequences for the design of eDNA monitoring programmes targeting conservation-priority taxa, and clear priorities for taxa specific reference-database expansion.

Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, exhibiting an uneven distribution across all 20 chromosomes. These C3H-ZFPs contained one (37), two (58), three (19), four (7), five (17), or six (2) C3H domains and were classified into 14 subsets based on their domain architecture. All C3H genes encoding proteins harbored the conserved C3H-ZFP domain and displayed various physicochemical characteristics. Phylogenetic analysis grouped them into 10 clades, closely related to other species like Arabidopsis, rice and alfalfa. Promoter analysis revealed cis-elements associated with stress response (~39.1%), light response (~37.3%), phytohormones (~18.5%), and development (~4.97%). Duplication analysis revealed 78 pairs of segmental and eight tandem duplication events, with purifying selection indicated by Ka/Ks (nonsynonymous/synonymous) ratios, indicating that these C3H-ZFP duplicates were largely maintained under purifying selection. A total of 388 miRNAs from 196 gene families were predicted to target 140 C3H-ZFP genes, with most enriched miRNAs targeting C3H-ZFP genes, including the miR156, miR395, and miR396 families. Transcription factor binding sites for MYB, AP2, MIKC_MADS, BBR-BPC, ERF, C2H2, and Dof were found upstream of most C3H-ZFP genes. RNA-Seq and qRT-PCR analyses showed tissue-specific expression and stress-responsive expression patterns, with several C3H-ZFP genes, especially GmC3H1, GmC3H63, GmC3H124, and GmC3H127, being significantly upregulated under abiotic stress conditions. Together, these results provide a comprehensive overview of soybean C3H-ZFP genes and identify promising candidates for future functional studies on development and abiotic stress adaptation.

Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA’s mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions. During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1

Despite extensive research on sphingolipid metabolism in Arabidopsis thaliana, the involvement of this pathway in major crop species, including rapeseed, rice, maize, soybean, and cotton, remains poorly understood. This knowledge gap presents an opportunity to explore sphingolipid biosynthesis in these crops, with the potential to identify novel, crop-specific sphingolipids that regulate yield-related traits. Sphingolipids are key regulators of plant responses to abiotic stresses such as drought, salinity, and freezing, as well as biotic interactions, including disease resistance and plant-microbe communication. Given their critical roles in plant physiology, sphingolipid pathways represent promising targets for enhancing stress resilience and optimizing crop productivity, offering new strategies for sustainable agriculture to meet the challenges of a growing global population. We have also listed the predicted homologs/orthologues of the pathway genes in rapeseed, soybean, rice, maize, and cotton based on amino acid sequence alignment score with Arabidopsis. This review provides an outline for projecting sphingolipid metabolic pathways across major crops, and enabling the prioritization of target genes to enhance key agronomic traits.

Pseudomonas argentinensis SA190 is a desert-adapted, plant-associated bacterium with demonstrated potential to enhance plant growth under abiotic stress. In this study, we conducted a comprehensive genomic and functional characterization of SA190 to uncover the molecular mechanisms underlying its biofilm formation, root colonization, and plant growth-promoting traits. The SA190 genome consists of a single circular chromosome (5.07 Mb, 64

Accumulating evidence indicates that microorganisms respond to the ubiquitous plastic pollution by evolving plastic-degrading enzymes. However, the functional diversity of these enzymes and their distribution across the ocean, including the deep sea, remain poorly understood. By integrating bioinformatics and artificial intelligence-based structure prediction, we developed a structure- and function-informed algorithm to computationally distinguish functional polyethylene terephthalate-degrading enzymes (PETases) from variants lacking PETase activity (pseudo-PETase), either due to alternative substrate specificity or pseudogene origin. Through in vitro functional screening and in vivo microcosm experiments, we verified that this algorithm identified a high-confidence, searchable sequence motif for functional PETases capable of degrading PET. Metagenomic analysis of 415 ocean samples revealed 23 PETase variants, detected in nearly 80% of the samples. These PETases mainly occur between 1,000 and 2,000 m deep and at the surface in regions with high plastic pollution. Metatranscriptomic analysis further identified PETase variants that were actively transcribed by marine microorganisms. In contrast to their terrestrial counterparts-where PETases are taxonomically diverse-those in marine ecosystems were predominantly encoded and transcribed by members of the Pseudomonadales order. Our study underscores the widespread distribution of PETase-containing bacteria across carbon-limited marine ecosystems, identifying and distinguishing the PETase motif that underpins the functionality of these specialized cutinases.

Background:Attempts to develop an hRSV vaccine have faced safety and efficacy challenges, with only three FDA-approved vaccines (Moderna's Mresvia, Pfizer's Abrysvo, and GSK's Arexvy) available. These vaccines are limited to individuals over 60 years, require boosters, and only reduce disease severity without clearing the infection. Therefore, we employed a reverse vaccinology approach in this study to identify the most promising antigenic epitopes capable of eliciting a robust and protective immune response. Methodology:This study employed computational techniques to design a novel multi-epitope vaccine targeting hRSV. Using bioinformatics tools, candidate epitopes were identified from conserved viral proteins (F and G glycoproteins), assessing their immunogenicity, antigenicity, and allergenicity. Key tools included ExPASy, ProtParam, VaxiJen v2.0, AllergenFP v1.0, AllerTOP v2.0, NetCTL v1.2, IEDB, and Toxin-Pred. The vaccine construct was assessed for stability and toxicity through in silico analyses. We then characterized its kinetic properties, evaluated its structural integrity, and analyzed its interactions with Toll-like receptors (TLRs) using molecular docking, modeling, and refinement with AlphaFold3 and ClusPro. Results:The designed constructs showed strong antigenicity (0.5996 for F-based and 0.6048 for G-based vaccine), non-allergenicity, and stability (instability index <40). Among these, most amino acids were in the extracellular domain of the construct. Molecular docking and dynamics simulations indicated strong binding interactions with TLR1 and TLR4 and minimal RMSF fluctuations, which ensured structural stability. Strong humoral and cellular responses were suggested by in silico immune simulation demonstrating robust immune activation, with high levels of IgG, IgM, IL-2, and IFN-γ. The physical and chemical analyses revealed that the majority of amino acids from the F and G proteins were located in the extracellular domain of the construct. The presence of signal peptide cleavage sites in both glycoprotein components further facilitates antigen presentation to the immune system. Conclusions:This study presents a promising peptide-based vaccine candidate against hRSV that can effectively engage the immune system, showing strong immunogenicity and antigenicity. Future in vitro and in vivo studies are essential to evaluate the ability of the multi-epitope vaccine candidate to stimulate both humoral and cell-mediated immune responses and to assess its efficacy and safety profile.

BACKGROUND:This study investigated the inflammatory and gut microbiota profile in chronic kidney disease (CKD) patients undergoing hemodialysis (HD) and peritoneal dialysis (PD). METHODS:A total of 249 patients undergoing HD and 61 patients on PD participated in the study. The mRNA expressions of nuclear factor erythroid 2-related factor-2 (NRF2), nuclear factor-κappa B (NF-κB), mitochondrial transcription factor A (TFAM), peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC-1α) were evaluated in peripheral blood mononuclear cells (PBMCs) by quantitative real-time PCR. Malondialdehyde (MDA), interleukin 6 (IL-6), and routine biochemical parameters were also analyzed. The fecal DNA extraction was performed, and the V4 regions of the bacterial 16S ribosomal RNA gene were sequenced. Uremic toxins such as p-cresyl sulfate (p-CS), indoxyl sulfate (IS), and indole-3-acetic acid (IAA) plasma levels were determined by HPLC. RESULTS:MDA, IS, and p-CS levels were lower in PD than in HD patients. The mRNA expression of the transcription factors was not different between groups. Gut microbial α-diversity indices showed no significant difference between groups, but the β-diversity was different in PD patients. Members of the genera Meditarraneibacter, Roseburia, Agathobacter, Anaerobutyricum, Collinsella, Streptococcus, Clostridium, and Bacteroides, as well as the families Lachnospiraceae and Enterobacteriaceae, appear to be positively correlated with most dietary factors, particularly lipid and phosphorus intake. CONCLUSIONS:Our findings indicate that in patients with CKD on HD, there is increased plasma retention of uremic toxins and reduced gut microbial diversity compared to PD patients.

Monosaccharide transporters (MSTs) are important plant glucose transporters that play roles in carbon allocation, growth, development, and stress regulation. However, research on MST regulatory genes in soybeans remains unexplored. In this study, we identified 110 MST-like candidate genes in the Glycine max L. (soybean) genome. The MST genes were distributed throughout 20 chromosomes, with many undergoing segmental duplication. The majority of MST group proteins exhibit significant preservation in Arabidopsis and soybean, and phylogenetic analysis reveals seven main categories. The promoters of the GmMST genes comprise cis-acting elements associated with plant responses to abscisic acid, auxin signaling, methyl jasmonate, low temperatures, and abiotic stresses. The RNA-seq data demonstrated diverse expression levels of MST genes across various tissues or organs, categorizing them into 11 primary clusters. The co-expression study of the network complex indicated that the GmMST genes encode proteins that interact with many essential genes associated with gibberellin, which are pivotal in seed and stamen development. A qPCR study validated the expression patterns of seven MST genes with exposure to copper (Cu) and cadmium (Cd) stress. Certain MST genes were notably stimulated by both Cu and Cd stress treatments, suggesting their involvement in defense responsiveness. Therefore, we provide a comprehensive analysis of the MST genes in soybeans and emphasize their substantial role in plant development and tolerance to metal ion stressors.

Hydrothermal vents along mid-ocean ridges host diverse microbial communities and are crucial to global elemental cycling. The Red Sea, known for its unique environmental conditions—including low nutrient levels, high year-round temperatures, bottom-water temperatures of 21 °C, and elevated salinity—hosts recently discovered active low-temperature hydrothermal vent fields at the axial Hatiba Mons volcano. These vents, characterized by large iron oxide mounds and abundant microbial mats, offer an extreme environment for studying the diversity and functions of prokaryotes involved in elemental cycling in this system. In this study, we used 16S rRNA sequencing and shotgun metagenomics to examine the microbial diversity and metabolic capabilities of precipitates and microbial mats from five vent sites. We recovered 314 non-redundant metagenome-assembled genomes (MAGs), including 250 bacterial and 64 archaeal MAGs, representing 34 bacterial and 11 archaeal phyla. Functional annotations revealed diverse nutrient and metal cycling potentials, with notable enrichment in iron redox genes. Key players include Bathyarchaeia and Chloroflexi in the precipitates (contributing to carbon, nitrogen, sulfur, and metal cycling potentials) and Pseudomonadota members in the microbial mats and upper precipitates (involved in iron and sulfur metabolism and carbon fixation through the CBB cycle). Carbon fixation in precipitate potentials primarily occurs through the Wood–Ljungdahl pathway. Sulfur and nitrogen cycling genes are distributed across various genomes, indicating collaborative cycling. Our genome-resolved analysis positions the Hatiba Mons vents as an iron-rich system that provides new insights into oligotrophic hydrothermal environments, with potential relevance for understanding novel metabolic pathways, extremophilic adaptations, and their roles in element cycling and biotechnological applications.

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line. The Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYLTRANSFERASE1 (CLAMT1) genes, which may contribute to SL biosynthesis. Functional assays show that P10CLAMT1b produces the SL-biosynthesis intermediate methyl carlactonoate (MeCLA) and that MeCLA is the precursor of P10-specific SLs. Screening a diverse pearl millet panel confirms the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification. Production of pearl millet is impacted by the root parasitic weed Striga hermonthica. Here, the authors assemble the genomes of resistant and susceptible lines of pearl millet and identify a critical gene CARLACTONOIC ACID METHYLTRANSFERASE1b (CLAMT1b) in determining Striga resistance.

The seed development is a crucial step in ensuring a healthy fruit set, and the ultimate seed size is a significant quality feature in fruit crops. Litchi seed development is a fascinating process because of its remarkable plasticity. Previous study has indicated that the partial seed abortion phenotype of litchi cv. ‘Guiwei’ is induced by thermo-sensitive sterility and self-sterility. The comprehension of how genetic background and temperature influence the litchi seed development is limited. Here, we target LcASHR1, a putative histone-lysine N-methyltransferase gene that was shown to be more highly expressed in the large seed cultivar ‘Huaizhi’ than in the small seed cultivar ‘Guiwei’. In addition, it was found to be enhanced in response to low temperatures, therefore aiding in the growth of the seeds. The knockdown of LcASHR1 in litchi resulted in tiny seeds and a higher level of seed abortion rate. Conversely, overexpression of LcASHR1 in Arabidopsis lines led to the production of larger seeds. Furthermore, LcTRB1, a putative telomere repeats binding protein, was identified as an upstream transact factor of LcASHR1 by binding to the telo-boxes in the promoter. LcTRB1 expression pattern largely corresponded to litchi seed size. Consistent with previous findings on LcASHR1, it has been observed that LcTRB1 positively affects seed development in both litchi and Arabidopsis. Overall, our results indicated that LcTRB1 is linked with litchi seed development probably by modulating the expression of LcASHR1.

The WRKY gene family consists of unique transcription factors (TFs) found exclusively in plants. These TFs play a crucial role in regulating how plants respond to various abiotic stresses, such as saline-alkaline conditions, temperature fluctuations, drought, UV radiation and others. Scientists have been progressively studying the roles and mechanisms of WRKY in several plant species, including both model plants and essential agricultural crops. This study focus has emerged due to the understanding that alkaline and saline soil stressors considerably impede global agricultural productivity. Multiple research efforts have underscored the significant biological functions of WRKY TFs in assisting plants in coping with various abiotic challenges, particularly in enhancing their ability to withstand alkaline-salt stress. This review aims to investigate the structural capabilities of WRKY TFs and their impact on plant responses to alkaline and salt stresses. Additionally, it seeks to elucidate the role of these TFs in alleviating diverse abiotic and biotic stressors. The objective of this review study is to provide comprehensive insights into the current state of the field and the importance of WRKY TFs in regulating plant responses to salt and alkaline stress.

The global ocean genome (the pool of genes in marine organisms and the functional information they encode) is a major, untapped resource for science and society with a growing range of biotechnology applications in sectors such as biomedicine, energy, and food. Shotgun sequencing and metagenomics can now be used to catalog the diversity of ocean microbial life and to explore its functional potential, but has been limited by sample coverage, access to suitable sequencing platforms, and computational capacity. Here we provide a novel synthesis of the global ocean genome based on analysis of 2,102 sampled ocean metagenomes, with gene assembly and annotation via the KAUST Metagenome Analysis Platform (KMAP) Global Ocean Gene Catalog 1.0 containing 308.6 million gene clusters. Taxonomically, we report the distribution of marine genes across the tree of life and different ocean basins and depth zone biomes. Functionally, we map its relationship to protein families and biogeochemical processes, including the major microbial metabolic pathways that process three elements that play fundamental roles in biogeochemical cycles and are relevant to climate change. These data extend our understanding of the complex, dynamic nature of the ocean microbiome and its metabolic capabilities. Further research is of critical global importance both to unlock the potential of the ocean genome and to understand and predict the effects of human-induced changes, including pollution and climate change. Further hypothesis-driven research should target under-sampled deep sea and benthic microbial communities using enhanced metagenomic methods, to better understand marine ecosystem functioning. Investment in the necessary computational capacity is essential, as are suitable intellectual property frameworks.

Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, Tara Oceans and Malaspina , that circumnavigated the oceans and sampled down to 4000 m to assess metazoans from environmental DNA (eDNA) extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer the relative abundance of phyla using metagenome datasets, and relate these data to environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related to metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean’s surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.

Salinity is an important abiotic stress that has an impact on crop yields and quality. Ubiquitin-mediated protein degradation enables plants to effectively withstand environmental stresses. The E3 ligases have been identified as a crucial component of the ubiquitination pathway, which regulates plant responses to abiotic stresses. The RING finger E3 ligase family of proteins has a critical role in plant growth and response to many abiotic stresses. In this study, we identified an important salt-responsive gene, BrRING509 in Brassica rapa. It is localized throughout the plasma membrane and nucleus. The functional results suggest that BrRING509 significantly increases salt stress tolerance in Arabidopsis (Arabidopsis thaliana) transgenic plants. Overexpression of BrRING509 could increase the survival and root length of transgenic seedlings under different salt concentrations. Additionally, ectopic expression of BrRING509 significantly increases the expression level of salt-responsive genes, including AtRD22 and AtRD29A in Arabidopsis transgenic plants subjected to salt stress treatments. The findings of this study indicate that BrRING509 plays a positive role in salt stress tolerance and might be an important candidate gene for the adaptation of Brassica plants in salt-stress environments.

Global climate change is closely related to changes in precipitation and flood events. In recent decades, waterlogging stress has become a greater threat to major crops and plants, ultimately affecting plant growth, development, and productivity. When plants are subjected to waterlogging, the oxygen supply in their roots is diminished, leading to hypoxic or anoxic conditions. To adapt to these conditions, plants go through a variety of physiological, morphological, and biochemical changes. This may involve the development of adventitious roots (ARs) and aerenchyma tissue, changes in the regulations of hormones, and shifts in metabolism. Specific genes and signaling pathways are essential for the coordination of these adaptive responses. Studies at the molecular level have significantly improved our understanding of the mechanisms by which plants respond to waterlogging stress. Identifying metabolic pathways and potential target genes is key to improving waterlogging tolerance in crops. Priority should be given to further research to uncover the gene regulatory networks and functional characterization of important genes involved in waterlogging tolerance. Furthermore, novel techniques, such as gene editing and breeding, can develop more resilient crop varieties to waterlogging stress. This review article discusses the current understanding of the molecular mechanisms underlying plant responses to waterlogging stress, as well as its effects on plant growth, development, and productivity. Furthermore, it discusses the potential future research challenges.