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Mule duck is vitally important to the production of global duck meat. Here, we present two high-quality haplotypes of a female mule duck (haplotype 1 (H1):1.28 Gb, haplotype 2 (H2): 1.40 Gb). The continuity (H1: contig N50 = 14.90 Mb, H2: contig N50 = 15.70 Mb) and completeness (BUSCO: H1 = 96.9%, H2 = 97.3%) are substantially better than those of other duck genomes. We detected the structural variations (SVs) in H1 and H2. We observed a positive correlation between autosome length and the number of SVs. Z chromosome was some deficient in deletions and insertions, but W chromosome was some excessive. A total of 1,451 genes were haplotype specific expression (HSEs). Among them, 737 specifically expressed in H1, and 714 specifically expressed in H2. We found that H1 and H2 HSEs tended to be involved in similar biological processes, such as myometrial relaxation and contraction pathways, muscle structure development and phosphorylation. Our haplotype-resolved genome assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in mule duck. [ABSTRACT FROM AUTHOR]

Incorporating adaptive traits from wild grape species will be essential for the future adaptability of viticulture. Long-read DNA sequencing and haplotype-aware assemblers have kickstarted wild grape genomics, overcoming high structural heterozygosity to reveal detailed haplotype diversity and structural variations. This progress has opened new avenues for the study of grape domestication and species adaptation. New diploid genome references have enabled the dissection of disease-resistance loci and advanced understanding of flower sex determination in grapes, clarifying the genetic shift from dioecy to hermaphroditism and pinpointing candidate sex-determining genes via haplotype analysis. Grape genomics is transitioning from single-reference to pangenomic approaches, enabling novel methodologies such as pan-genome-wide association studies and enhancing our understanding and utilization of grape genetic resources. With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement. [ABSTRACT FROM AUTHOR]

There is remarkable genetic diversity throughout the human population, but variant interpretation lags far behind discovery. As a result, most genetic variation is not clinically actionable. Single-cell sequencing provides a high-throughput, disease- and pathway-agnostic means to profile variant effects with mechanistic detail across the entire regulatory cascade. Many single-cell genomics methods have been coupled to CRISPR-based gene disruption, but these techniques are rapidly expanding to accommodate increasingly diverse types of perturbations including missense variants, protein fusions, structural variants, genetic circuits, chemical perturbations, and increasingly their combinations. High-throughput, deep phenotyping of genetic variation will allow researchers to define causal mechanisms and nominate precision therapeutics for controlling cell states. Population-scale sequencing efforts have catalogued substantial genetic variation in humans such that variant discovery dramatically outpaces interpretation. We discuss how single-cell sequencing is poised to reveal genetic mechanisms at a rate that may soon approach that of variant discovery. The functional genomics toolkit is sufficiently modular to systematically profile almost any type of variation within increasingly diverse contexts and with molecularly comprehensive and unbiased readouts. As a result, we can construct deep phenotypic atlases of variant effects that span the entire regulatory cascade. The same conceptual approach to interpreting genetic variation should be applied to engineering therapeutic cell states. In this way, variant mechanism discovery and cell state engineering will become reciprocating and iterative processes towards genomic medicine. [ABSTRACT FROM AUTHOR]

SUMMARY: The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome‐scale haplotype‐resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor‐AA and Ancestor‐BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high‐quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics. Significance Statement: Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. [ABSTRACT FROM AUTHOR]

Background: The human epididymis is poorly studied due to the lack of availability of tissue samples. Our understanding of its structure and function depends upon anatomical and histological observations of archived material. Objectives: Here we used single‐cell RNA sequencing (scRNA‐seq) technologies to elucidate the identity of cells within the human efferent ducts (EDs) and compared them to caput epididymis cells. We also compared the cellularity of primary tissues with those of 2D and 3D (organoid) culture models used for functional studies. Materials and methods: Human epididymis tissue was dissected to separate different anatomical regions and digested to release single cells for processing on the 10X Genomics Chromium platform. Primary human epididymis epithelial (HEE) cells and HEE organoids were grown as described previously and subjected to scRNA‐seq. scRNA‐seq data were processed by standard bioinformatics pipelines and used for comparative analysis. Results: We define the cell types in the EDs which include specialized epithelial cells, connective tissue stromal cells, vascular endothelial cells, smooth muscle cells, and immune cells, but lack basal cells that are seen in the caput epididymis. Furthermore, we identify a sub‐population of epithelial cells which have marker genes found in the bladder and urothelium. Comparative genomics analysis of the 2D and 3D culture models shows cellular identities adapted to the culture environment while still maintaining similarity to the primary tissue. Discussion: Our data suggest that EDs are lined with a transitional epithelium, which like the urothelium is able to stretch and contract depending on luminal volume. This is consistent with its primary role in seminal fluid resorption and sperm concentration. Moreover, we describe the cellularity of models to study the human epididymis epithelium in vitro. Conclusion: Single‐cell RNA‐seq data from the human epididymis make a valuable contribution to our understanding of this highly specialized organ. [ABSTRACT FROM AUTHOR]

Background: Sika deer (Cervus nippon) holds significance among cervids, with three genomes recently published. However, these genomes still contain hundreds of gaps and display significant discrepancies in continuity and accuracy. This poses challenges to functional genomics research and the selection of an appropriate reference genome. Thus, obtaining a high-quality reference genome is imperative to delve into functional genomics effectively. Findings: Here we report a high-quality consensus genome of male sika deer. All 34 chromosomes are assembled into single-contig pseudomolecules without any gaps, which is the most complete assembly. The genome size is 2.7G with 23,284 protein-coding genes. Comparative genomics analysis found that the genomes of sika deer and red deer are highly conserved, an approximately 2.4G collinear regions with up to 99% sequence similarity. Meanwhile, we observed the fusion of red deer's Chr23 and Chr4 during evolution, forming sika deer's Chr1. Additionally, we identified 607 transcription factors (TFs) that are involved in the regulation of antler development, including RUNX2, SOX6, SOX8, SOX9, PAX8, SIX2, SIX4, SIX6, SPI1, NFAC1, KLHL8, ZN710, JDP2, and TWST2, based on this consensus reference genome. Conclusions: Our results indicated that we acquired a high-quality consensus reference genome. That provided valuable resources for understanding functional genomics. In addition, discovered the genetic basis of sika-red hybrid fertility and identified 607 significant TFs that impact antler development. [ABSTRACT FROM AUTHOR]

The 36th International Mammalian Genome Conference (IMGC) was held in a hybrid format at the Tsukuba International Congress Center in Tsukuba, Ibaraki, Japan, for 4 days from March 28 to 31, 2023. This international conference on functional genomics of mouse, human, and other mammalian species attracted 246 participants in total, of which 129 were from outside Japan, including Europe, the United States and Asia, and 117 participants were from Japan. The conference included three technical workshops, keynote lectures by domestic researchers, commemorative lectures for the conference awards, 57 oral presentations, and 97 poster presentations. The event was a great success. Topics included the establishment and analysis of disease models using genetically engineered or spontaneous mutant mice, systems genetic analysis using mouse strains such as wild‐derived mice and recombinant inbred mouse strains, infectious diseases, immunology, and epigenetics. In addition, as a joint program, a two‐day RIKEN Symposium was held, and active discussions continued over the four‐day period. Also, there was a trainee symposium, in which young researchers were encouraged to participate, and excellent papers were selected as oral presentations in the main session. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa) faces challenges to yield and quality due to urbanisation, deforestation and climate change, which has exacerbated high night temperature (HNT). This review explores the impacts of HNT on the physiological, molecular and agronomic aspects of rice growth. Rise in minimum temperature threatens a potential 41% reduction in rice yield by 2100. HNT disrupts rice growth stages, causing reduced seed germination, biomass, spikelet sterility and poor grain development. Recent findings indicate a 4.4% yield decline for every 1°C increase beyond 27°C, with japonica ecotypes exhibiting higher sensitivity than indica. We examine the relationships between elevated CO2, nitrogen regimes and HNT, showing that the complexity of balancing positive CO2 effects on biomass with HNT challenges. Nitrogen enrichment proves crucial during the vegetative stage but causes disruption to reproductive stages, affecting grain yield and starch synthesis. Additionally, we elucidate the impact of HNT on plant respiration, emphasising mitochondrial respiration, photorespiration and antioxidant responses. Genomic techniques, including CRISPR-Cas9, offer potential for manipulating genes for HNT tolerance. Plant hormones and carbohydrate enzymatic activities are explored, revealing their intricate roles in spikelet fertility, grain size and starch metabolism under HNT. Gaps in understanding genetic factors influencing heat tolerance and potential trade-offs associated with hormone applications remain. The importance of interdisciplinary collaboration is needed to provide a holistic approach. Research priorities include the study of regulatory mechanisms, post-anthesis effects, cumulative HNT exposure and the interaction between climate variability and HNT impact to provide a research direction to enhance rice resilience in a changing climate. We explore the impact of high night temperature (HNT) on rice phenomics, physiology and grain yield. From accelerated vegetative growth to changes in reproductive phases and enzymatic activities, we review how HNT affects rice in elevated CO2 and nitrogen environments to provide insights into photosynthesis, respiration and hormonal regulation, and their effect on grain yield and quality. This article belongs to the Collection Functional Genomics for Developing Climate Resilient Crops. [ABSTRACT FROM AUTHOR]

The investigation into cysteine-rich receptor-like kinases (CRLKs) holds pivotal significance as these conserved, upstream signalling molecules intricately regulate fundamental biological processes such as plant growth, development and stress adaptation. This study undertakes a comprehensive characterisation of CRLKs in Solanum tuberosum (potato), a staple food crop of immense economic importance. Employing comparative genomics and evolutionary analyses, we identified 10 distinct CRLK genes in potato. Further categorisation into three major groups based on sequence similarity was performed. Each CRLK member in potato was systematically named according to its chromosomal position. Multiple sequence alignment and phylogenetic analyses unveiled conserved gene structures and motifs within the same groups. The genomic distribution of CRLKs was observed across Chromosomes 2–5, 8 and 12. Gene duplication analysis highlighted a noteworthy trend, with most gene pairs exhibiting a Ka/Ks ratio greater than one, indicating positive selection of StCRLKs in potato. Salt and drought stresses significantly impacted peroxidase and catalase activities in potato seedlings. The presence of diverse cis -regulatory elements, including hormone-responsive elements, underscored their involvement in myriad biotic and abiotic stress responses. Interestingly, interactions between the phytohormone auxin and CRLK proteins unveiled a potential auxin-mediated regulatory mechanism. A holistic approach combining transcriptomics and quantitative PCR validation identified StCRLK9 as a potential candidate involved in plant response to heat, salt and drought stresses. This study lays a robust foundation for future research on the functional roles of the CRLK gene family in potatoes, offering valuable insights into their diverse regulatory mechanisms and potential applications in stress management. Potato (Solanum tuberosum), the third-largest staple food crop, faces a major food security threat from environmental factors including salinity, temperature fluctuations and drought. We characterise the cysteine-rich receptor-like kinase (CRLK) gene family in potato, shedding light on its molecular mechanism in the complex interplay between plants and environmental stressors. The gene StCRLK9 may be involved in various abiotic stress responses. This establishes the groundwork for further investigations into the role of the potato CRLKs gene family in engineering climate resilient future crop plants. This article belongs to the Collection Functional Genomics for Developing Climate Resilient Crops. [ABSTRACT FROM AUTHOR]

This study explores the metabolic diversity of thermophilic Bacillus species isolated from Jordanian hot springs. Sixteen strains from Ma'en thermal springs, exhibiting robust growth at elevated temperatures (45-55°C), were investigated for their potential in producing valuable bioactive compounds. Crude extracts, obtained through organic solvent extraction, underwent HPLC-MS analysis to reveal secondary metabolite spectra under various growth conditions. Strains M5a, M13a, and M1c displayed potential in producing biologically active metabolites. The purification process of the M5a strain extracts involved sequential techniques including silica gel, Sephadex LH-20, RP18 column chromatography, and preparative TLC. This process resulted in the isolation of diverse compounds, including indole derivatives (1-acetyl-ß-carboline, indole-3-carboxylic acid, tryptophol), adenosine, tyrosol, p-hydroxy-benzaldehyde, ferulic acid, uracil, 3-methyl uracil, and the identification of four diketopiperazine derivatives (cyclo (Phe, Pro), cyclo (Pro, Ile), cyclo (Leu, Pro), and cyclo (Pro, Tyr)). Structural validation of these compounds was achieved through AntiBase, utilizing 1H NMR and MS data and literature comparisons. Despite similar metabolic profiles, strains exhibited varying activities, including antimicrobial potential. This study marks the first report on purified biochemical compounds from thermophilic bacteria, emphasizing untapped microbial diversity in thermal springs. Intriguing activities and distinct UV-absorbing bands on TLC suggest promising prospects for isolating novel, active metabolites. This research enhances our understanding of the biotechnological potential of thermophilic Bacillus strains, emphasizing the importance of exploring their chemodiversity for industrial applications and functional genomics. [ABSTRACT FROM AUTHOR]

Advances in analytical methods such as in machine learning have enabled rapid prioritization of noncoding variant effects. Emerging high-throughput screening methods such as massively parallel reporter assays and CRISPR-based approaches provide orthogonal interpretation of noncoding variant effects. Bona fide validation of noncoding variant effects remains challenging and necessitates observing an impact at the endogenous genomic locus. Genome-wide association studies (GWASs) provide a key foundation for elucidating the genetic underpinnings of common polygenic diseases. However, these studies have limitations in their ability to assign causality to particular genetic variants, especially those residing in the noncoding genome. Over the past decade, technological and methodological advances in both analytical and empirical prioritization of noncoding variants have enabled the identification of causative variants by leveraging orthogonal functional evidence at increasing scale. In this review, we present an overview of these approaches and describe how this workflow provides the groundwork necessary to move beyond associations toward genetically informed studies on the molecular and cellular mechanisms of polygenic disease. [ABSTRACT FROM AUTHOR]

Genome-wide association studies (GWAS) significantly enhance our ability to identify trait-associated genomic variants by considering the host genome. Moreover, the hologenome refers to the host organism's collective genetic material and its associated microbiome. In this study, we utilized the hologenome framework, called Hologenome-wide association studies (HWAS), to dissect the architecture of complex traits, including milk yield, methane emissions, rumen physiology in cattle, and gut microbial composition in pigs. We employed four statistical models: (1) GWAS, (2) Microbial GWAS (M-GWAS), (3) HWAS-CG (hologenome interaction estimated using COvariance between Random Effects Genome-based restricted maximum likelihood (CORE-GREML)), and (4) HWAS-H (hologenome interaction estimated using the Hadamard product method). We applied Bonferroni correction to interpret the significant associations in the complex traits. The GWAS and M-GWAS detected one and sixteen significant SNPs for milk yield traits, respectively, whereas the HWAS-CG and HWAS-H each identified eight SNPs. Moreover, HWAS-CG revealed four, and the remaining models identified three SNPs each for methane emissions traits. The GWAS and HWAS-CG detected one and three SNPs for rumen physiology traits, respectively. For the pigs' gut microbial composition traits, the GWAS, M-GWAS, HWAS-CG, and HWAS-H identified 14, 16, 13, and 12 SNPs, respectively. We further explored these associations through SNP annotation and by analyzing biological processes and functional pathways. Additionally, we integrated our GWA results with expression quantitative trait locus (eQTL) data using transcriptome-wide association studies (TWAS) and summary-based Mendelian randomization (SMR) methods for a more comprehensive understanding of SNP-trait associations. Our study revealed hologenomic variability in agriculturally important traits, enhancing our understanding of host-microbiome interactions. [ABSTRACT FROM AUTHOR]

Objective: To characterize the scalp microbial composition, function, and connection to dandruff severity using a metagenomics approach and to understand the impact of a Piroctone Olamine containing anti‐dandruff shampoo on the scalp microbiome. Methods: Shotgun metagenomics was used to characterize the composition of the scalp microbiomes from 94 subjects with and without clinically defined dandruff. Furthermore, the microbiome of the scalps of 100 dandruff sufferers before and after 3 weeks of treatment with either control or anti‐dandruff shampoo containing 0.5% Piroctone Olamine (PO) was characterized and compared to identify microorganisms associated with the dandruff condition and the associated pathways and processes that may contribute to PO's effect on scalp microbiome. Results: A higher relative abundance of Malassezia restricta and Staphylococcus capitis and a lower abundance of Cutibacterium acnes were associated with the dandruff scalps relative to the no‐dandruff scalps. A 3‐week PO shampoo treatment reduced the relative abundance of Malassezia species and Staphylococcus capitis and increased the relative abundance of Cutibacterium acnes. This change to the scalp microbiome composition is consistent with a return to a healthy no‐dandruff microbiome and improved clinical signs and symptoms as measured by adherent scalp flaking score (ASFS) compared with the control shampoo. Functional genomics analysis showed that the PO shampoo treatment reduced oxidative stress‐associated genes and decreased the abundance of protease, urease, and lipase genes. These changes correlated positively to improvements in dandruff severity. PO treatment favourably shifted scalp microbiomes in dandruff subjects toward the no‐dandruff state. Conclusion: Our results suggest that part of the aetiology of dandruff can be attributed to dysbiosis of the scalp microbiome. PO treatment can restore a healthier microbiome, reducing oxidative stress and promoting better scalp health. [ABSTRACT FROM AUTHOR]

Background: The red oleaginous yeast Rhodotorula toruloides is a promising cell factory to produce microbial oils and carotenoids from lignocellulosic hydrolysates (LCH). A multi-stress tolerant strain towards four major inhibitory compounds present in LCH and methanol, was derived in our laboratory from strain IST536 (PYCC 5615) through adaptive laboratory evolution (ALE) under methanol and high glycerol selective pressure. Results: Comparative genomic analysis suggested the reduction of the original strain ploidy from triploid to diploid, the occurrence of 21,489 mutations, and 242 genes displaying copy number variants in the evolved strain. Transcriptomic analysis identified 634 genes with altered transcript levels (465 up, 178 down) in the multi-stress tolerant strain. Genes associated with cell surface biogenesis, integrity, and remodelling and involved in stress-responsive pathways exhibit the most substantial alterations at the genome and transcriptome levels. Guided by the suggested stress responses, the multi-stress tolerance phenotype was extended to osmotic, salt, ethanol, oxidative, genotoxic, and medium-chain fatty acid-induced stresses. Conclusions: The comprehensive analysis of this evolved strain provided the opportunity to get mechanistic insights into the acquisition of multi-stress tolerance and a list of promising genes, pathways, and regulatory networks, as targets for synthetic biology approaches applied to promising cell factories, toward more robust and superior industrial strains. This study lays the foundations for understanding the mechanisms underlying tolerance to multiple stresses in R. toruloides, underscoring the potential of ALE for enhancing the robustness of industrial yeast strains. [ABSTRACT FROM AUTHOR]

Premature ovarian insufficiency is a common form of female infertility affecting up to 4% of women and characterised by amenorrhea with elevated gonadotropin before the age of 40. Oocytes require controlled DNA breakage and repair for homologous recombination and the maintenance of oocyte integrity. Biallelic disruption of the DNA damage repair gene, Fanconi anemia complementation group A (FANCA), is a common cause of Fanconi anaemia, a syndrome characterised by bone marrow failure, cancer predisposition, physical anomalies and POI. There is ongoing dispute about the role of heterozygous FANCA variants in POI pathogenesis, with insufficient evidence supporting causation. Here, we have identified biallelic FANCA variants in French sisters presenting with POI, including a novel missense variant of uncertain significance and a likely pathogenic deletion that initially evaded detection. Functional studies indicated no discernible effect on DNA damage sensitivity in patient lymphoblasts. These novel FANCA variants add evidence that heterozygous loss of one allele is insufficient to cause DNA damage sensitivity and POI. We propose that intragenic deletions, that are relatively common in FANCA, may be missed without careful analysis, and could explain the presumed causation of heterozygous variants. Accurate variant curation is critical to optimise patient care and outcomes. [ABSTRACT FROM AUTHOR]

Psoriasis is a lifelong, systemic, immune mediated inflammatory skin condition, affecting 1–3% of the world's population, with an impact on quality of life similar to diseases like cancer or diabetes. Genetics are the single largest risk factor in psoriasis, with Genome-Wide Association (GWAS) studies showing that many psoriasis risk genes lie along the IL-23/Th17 axis. Potential psoriasis risk genes determined through GWAS can be annotated and characterised using functional genomics, allowing the identification of novel drug targets and the repurposing of existing drugs. This review is focused on the IL-23/Th17 axis, providing an insight into key cell types, cytokines, and intracellular signaling pathways involved. This includes examination of currently available biological treatments, time to relapse post drug withdrawal, and rates of primary/secondary drug failure, showing the need for greater understanding of the underlying genetic mechanisms of psoriasis and how they can impact treatment. This could allow for patient stratification towards the treatment most likely to reduce the burden of disease for the longest period possible. [ABSTRACT FROM AUTHOR]

Tef research has little benefited from omics due to neglect of the crop by the global scientific community. However, the few utilized tools showed promising results. Chromosome-scale assembly of the genome reveals the evolution of tef. The whole-genome sequencing of drought-resurrecting Eragrostis nindensis and desiccation-sensitive Eragrostis curvula shows genes that play key roles in drought responses. A few studies using omics tools have revealed differentially expressed genes, proteins, and metabolites in tef plants exposed to drought. Molecular markers have deciphered diversity in tef germplasm collected from diverse agroecologies in Ethiopia. The application of targeting induced local lesions in genomes resulted in mutant tef lines with a semidwarf stature, which were later bred to locally adapted and high-yielding varieties. Genome editing using 'Green Revolution' genes resulted in a semidwarf and lodging-tolerant tef plant. Tef or teff [ Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research. [ABSTRACT FROM AUTHOR]

In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome‐wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle. [ABSTRACT FROM AUTHOR]

Over 400 million years old, scorpions represent an ancient group of arachnids and one of the first animals to adapt to life on land. Presently, the lack of available genomes within scorpions hinders research on their evolution. This study leverages ultralong nanopore sequencing and Pore-C to generate the first chromosome-level assembly and annotation for the desert hairy scorpion, Hadrurus arizonensis. The assembled genome is 2.23 Gb in size with an N50 of 280 Mb. Pore-C scaffolding reoriented 99.6% of bases into nine chromosomes and BUSCO identified 998 (98.6%) complete arthropod single copy orthologs. Repetitive elements represent 54.69% of the assembled bases, including 872,874 (29.39%) LINE elements. A total of 18,996 protein-coding genes and 75,256 transcripts were predicted, and extracted protein sequences yielded a BUSCO score of 97.2%. This is the first genome assembled and annotated within the family Hadruridae, representing a crucial resource for closing gaps in genomic knowledge of scorpions, resolving arachnid phylogeny, and advancing studies in comparative and functional genomics. [ABSTRACT FROM AUTHOR]

The growing preference for incorporating microbial aspartic proteases in industries is due to their high catalytic function and high degree of substrate selectivity. These properties, however, are attributable to molecular alterations in their structure and a variety of other characteristics. Molecular tools, functional genomics, and genome editing technologies coupled with other biotechnological approaches have aided in improving the potential of industrially important microbial proteases by addressing some of their major limitations, such as: low catalytic efficiency, low conversion rates, low thermostability, and less enzyme yield. However, the native folding within their full domain is dependent on a surrounding structure which challenges their functionality in substrate conversion, mainly due to their mutual interactions in the context of complex systems. Hence, manipulating their structure and controlling their expression systems could potentially produce enzymes with high selectivity and catalytic functions. The proteins produced by microbial aspartic proteases are industrially capable and far-reaching in regulating certain harmful distinctive industrial processes and the benefits of being eco-friendly. This review provides: an update on current trends and gaps in microbial protease biotechnology, exploring the relevant recombinant strategies and molecular technologies widely used in expression platforms for engineering microbial aspartic proteases, as well as their potential industrial and biotechnological applications. [ABSTRACT FROM AUTHOR]

Simple Summary: Editing (deletion, insertion, and substitution) of target genes is a commonly used method for studying gene function, which has significant applications in disease treatment, agricultural improvement, and environmental protection. The CRISPR/Cas9 system is currently the most widely used gene-editing technology due to its low cost and high efficiency. Continuous improvements in this system by researchers have resulted in a wide range of applications and greatly advanced gene function research. However, many CRISPR/Cas9 systems are complex and difficult to share, limiting their use to a few laboratories. In this study, we present a simple, low-cost, and universal CRISPR/Cas9 knockout system. We provide detailed information on the plasmid sequences, reagent codes, and methods. This study can help researchers establish gene knockout systems and facilitate better gene function research. The CRISPR/Cas9 gene-editing system is a standard technique in functional genomics, with widespread applications. However, the establishment of a CRISPR/Cas9 system is challenging. Previous studies have presented numerous methodologies for establishing a CRISPR/Cas9 system, yet detailed descriptions are limited. Additionally, the difficulties in obtaining the necessary plasmids have hindered the replication of CRISPR/Cas9 techniques in other laboratories. In this study, we share a detailed and simple CRISPR/Cas9 knockout system with optimized steps. The results of gene knockout experiments in vitro and in vivo show that this system successfully knocked out the target gene. By sharing detailed information on plasmid sequences, reagent codes, and methods, this study can assist researchers in establishing gene knockout systems. [ABSTRACT FROM AUTHOR]

Metabolic dysfunction-associated steatotic liver disease affects millions of people worldwide. Progress towards a definitive cure has been incremental and treatment is currently limited to lifestyle modification. Hepatocyte-specific lipid accumulation is the main trigger of lipotoxic events, driving inflammation and fibrosis. The underlying pathology is extraordinarily heterogenous, and the manifestations of steatohepatitis are markedly influenced by metabolic communications across non-hepatic organs. Synthetic human tissue models have emerged as powerful platforms to better capture the mechanistic diversity in disease progression, while preserving person-specific genetic traits. In this review, we will outline current research efforts focused on integrating multiple synthetic tissue models of key metabolic organs, with an emphasis on organoid-based systems. By combining functional genomics and population-scale en masse profiling methodologies, human tissues derived from patients can provide insights into personalised genetic, transcriptional, biochemical, and metabolic states. These collective efforts will advance our understanding of steatohepatitis and guide the development of rational solutions for mechanism-directed diagnostic and therapeutic investigation. [ABSTRACT FROM AUTHOR]

Mutagenesis has been one of the effective methods for creating genetic diversity and plant mutants can be significant bio-resources for crop breeding and functional genomics studies. The genetic and phenotypic diversity of 95 selected mutants from 17 mutant populations, obtained from an EMS mutagenized rice Hashemi variety, were phenotypically and molecularly assessed in M3 generation. Phenotypic variation of these mutants showed that grain yield components varied among the selected mutants compared to the control plants. In parallel, genetic diversity assessed by 13 Inter-Simple Sequence Repeats (ISSR) primers showed that the number of amplified fragments per primer varied from 4 (pr1-7) to 11 (ISSR-7, ISSR-11). In general, 13 primers amplified 99 fragments, 50 of which were polymorphic (52.92%). The genetic variation created by ISSR markers within 17 populations varied from 11.11% in HM9 (Hashemi Mutant Line number 9) to 45.45% in HM2. The average molecular polymorphism value was 0.27. In the total genetic variance, 95% of differences were attributed to within-population diversity, and 5% were related to among-populations. The Unweighted Pair-Group Method with Arithmetic mean (UPGMA) trees illustrating ISSR diversity classified the rice mutant population into seven groups, which were further supported by model-based STRUCTURE analysis. In general, the studied mutant genotypes revealed desirable genetic characteristics in populations 13 and 17, with em3h204 and em3h280 genotypes being the most divergent. [ABSTRACT FROM AUTHOR]

The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages—eggs, larvae, and adults—gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia's cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector. [ABSTRACT FROM AUTHOR]

Background: In recent years, Single-cell RNA sequencing (scRNA-seq) is increasingly accessible to researchers of many fields. However, interpreting its data demands proficiency in multiple programming languages and bioinformatic skills, which limited researchers, without such expertise, exploring information from scRNA-seq data. Therefore, there is a tremendous need to develop easy-to-use software, covering all the aspects of scRNA-seq data analysis. Results: We proposed a clear analysis framework for scRNA-seq data, which emphasized the fundamental and crucial roles of cell identity annotation, abstracting the analysis process into three stages: upstream analysis, cell annotation and downstream analysis. The framework can equip researchers with a comprehensive understanding of the analysis procedure and facilitate effective data interpretation. Leveraging the developed framework, we engineered Shaoxia, an analysis platform designed to democratize scRNA-seq analysis by accelerating processing through high-performance computing capabilities and offering a user-friendly interface accessible even to wet-lab researchers without programming expertise. Conclusion: Shaoxia stands as a powerful and user-friendly open-source software for automated scRNA-seq analysis, offering comprehensive functionality for streamlined functional genomics studies. Shaoxia is freely accessible at http://www.shaoxia.cloud, and its source code is publicly available at https://github.com/WiedenWei/shaoxia. [ABSTRACT FROM AUTHOR]

Background: Sweet yellow clover (Melilotus officinalis) is a diploid plant (2n = 16) that is native to Europe. It is an excellent legume forage. It can both fix nitrogen and serve as a medicine. A genome assembly of Melilotus officinalis that was collected from Best corporation in Beijing is available based on Nanopore sequencing. The genome of Melilotus officinalis was sequenced, assembled, and annotated. Results: The latest PacBio third generation HiFi assembly and sequencing strategies were used to produce a Melilotus officinalis genome assembly size of 1,066 Mbp, contig N50 = 5 Mbp, scaffold N50 = 130 Mbp, and complete benchmarking universal single-copy orthologs (BUSCOs) = 96.4%. This annotation produced 47,873 high-confidence gene models, which will substantially aid in our research on molecular breeding. A collinear analysis showed that Melilotus officinalis and Medicago truncatula shared conserved synteny. The expansion and contraction of gene families showed that Melilotus officinalis expanded by 565 gene families and shrank by 56 gene families. The contacted gene families were associated with response to stimulus, nucleotide binding, and small molecule binding. Thus, it is related to a family of genes associated with peptidase activity, which could lead to better stress tolerance in plants. Conclusions: In this study, the latest PacBio technology was used to assemble and sequence the genome of the Melilotus officinalis and annotate its protein-coding genes. These results will expand the genomic resources available for Melilotus officinalis and should assist in subsequent research on sweet yellow clover plants. [ABSTRACT FROM AUTHOR]

Background: Biofilm formation is viewed as a vital mechanism in C. glabrata pathogenesis. Although, it plays a significant role in virulence but transcriptomic architecture and metabolic pathways governing the biofilm growth mode of C. glabrata remain elusive. The present study intended to investigate the genes implicated in biofilm growth phase of C. glabrata through global transcriptomic approach. Results: Functional analysis of Differentially expressed genes (DEGs) using gene ontology and pathways analysis revealed that upregulated genes are involved in the glyoxylate cycle, carbon-carbon lyase activity, pre-autophagosomal structure membrane and vacuolar parts whereas, down- regulated genes appear to be associated with glycolysis, ribonucleoside biosynthetic process, ribosomal and translation process in the biofilm growth condition. The RNA-Seq expression of eight selected DEGs (CgICL1, CgMLS1, CgPEP1, and CgNTH1, CgERG9, CgERG11, CgTEF3, and CgCOF1) was performed with quantitative real-time PCR (RT-qPCR). The gene expression profile of selected DEGs with RT-qPCR displayed a similar pattern of expression as observed in RNA-Seq. Phenotype screening of mutant strains generated for genes CgPCK1 and CgPEP1, showed that Cgpck1∆ failed to grow on alternative carbon substrate (Glycerol, Ethanol, Oleic acid) and similarly, Cgpep1∆ unable to grow on YPD medium supplemented with hydrogen peroxide. Our results suggest that in the absence of glucose, C. glabrata assimilate glycerol, oleic acid and generate acetyl coenzyme-A (acetyl-CoA) which is a central and connecting metabolite between catabolic and anabolic pathways (glyoxylate and gluconeogenesis) to produce glucose and fulfil energy requirements. Conclusions: The study was executed using various approaches (transcriptomics, functional genomics and gene deletion) and it revealed that metabolic plasticity of C. glabrata (NCCPF-100,037) in biofilm stage modulates its virulence and survival ability to counter the stress and may promote its transition from commensal to opportunistic pathogen. The observations deduced from the present study along with future work on characterization of the proteins involved in this intricate process may prove to be beneficial for designing novel antifungal strategies. [ABSTRACT FROM AUTHOR]

Summary: Background: Microglia, the brain's resident immune cells, play vital roles in brain development, and disorders like Alzheimer's disease (AD). Human iPSC-derived microglia (iMG) provide a promising model to study these processes. However, existing iMG generation protocols face challenges, such as prolonged differentiation time, lack of detailed characterization, and limited gene function investigation via CRISPR-Cas9. Methods: Our integrated toolkit for in-vitro microglia functional genomics optimizes iPSC differentiation into iMG through a streamlined two-step, 20-day process, producing iMG with a normal karyotype. We confirmed the iMG's authenticity and quality through single-cell RNA sequencing, chromatin accessibility profiles (ATAC-Seq), proteomics and functional tests. The toolkit also incorporates a drug-dependent CRISPR-ON/OFF system for temporally controlled gene expression. Further, we facilitate the use of multi-omic data by providing online searchable platform that compares new iMG profiles to human primary microglia: https://sherlab.shinyapps.io/IPSC-derived-Microglia/. Results: Our method generates iMG that closely align with human primary microglia in terms of transcriptomic, proteomic, and chromatin accessibility profiles. Functionally, these iMG exhibit Ca2 + transients, cytokine driven migration, immune responses to inflammatory signals, and active phagocytosis of CNS related substrates including synaptosomes, amyloid beta and myelin. Significantly, the toolkit facilitates repeated iMG harvesting, essential for large-scale experiments like CRISPR-Cas9 screens. The standalone ATAC-Seq profiles of our iMG closely resemble primary microglia, positioning them as ideal tools to study AD-associated single nucleotide variants (SNV) especially in the genome regulatory regions. Conclusions: Our advanced two-step protocol rapidly and efficiently produces authentic iMG. With features like the CRISPR-ON/OFF system and a comprehensive multi-omic data platform, our toolkit equips researchers for robust microglial functional genomic studies. By facilitating detailed SNV investigation and offering a sustainable cell harvest mechanism, the toolkit heralds significant progress in neurodegenerative disease drug research and therapeutic advancement. [ABSTRACT FROM AUTHOR]

Parkinson's disease is a progressive neurological disorder, characterized by prominent movement dysfunction. The past two decades have seen a rapid expansion of our understanding of the genetic basis of Parkinson's, initially through the identification of monogenic forms and, more recently, through genome-wide association studies identifying common risk variants. Intriguingly, a number of cellular pathways have emerged from these analysis as playing central roles in the aetiopathogenesis of Parkinson's. In this review, the impact of data deriving from genome-wide analyses for Parkinson's upon our functional understanding of the disease will be examined, with a particular focus on examples of endo-lysosomal and mitochondrial dysfunction. The challenges of moving from a genetic to a functional understanding of common risk variants for Parkinson's will be discussed, with a final consideration of the current state of the genetic architecture of the disorder. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'. [ABSTRACT FROM AUTHOR]

Wilms tumor (WT) is the most common renal malignancy of childhood. Despite improvements in the overall survival, relapse occurs in ~15% of patients with favorable histology WT (FHWT). Half of these patients will succumb to their disease. Identifying novel targeted therapies remains challenging in part due to the lack of faithful preclinical in vitro models. Here we establish twelve patient-derived WT cell lines and demonstrate that these models faithfully recapitulate WT biology using genomic and transcriptomic techniques. We then perform loss-of-function screens to identify the nuclear export gene, XPO1, as a vulnerability. We find that the FDA approved XPO1 inhibitor, KPT-330, suppresses TRIP13 expression, which is required for survival. We further identify synergy between KPT-330 and doxorubicin, a chemotherapy used in high-risk FHWT. Taken together, we identify XPO1 inhibition with KPT-330 as a potential therapeutic option to treat FHWTs and in combination with doxorubicin, leads to durable remissions in vivo. A functional genomics approach in patient derived cell lines of Favorable Histology Wilms Tumor identifies suppression of TRIP13 through the nuclear export inhibitor, KPT-330, leads to decreased viability and synergy with doxorubicin. [ABSTRACT FROM AUTHOR]

Evechinus chloroticus (commonly known as kina) is a sea urchin species endemic to New Zealand. Its roe is a culinary delicacy to the indigenous Māori and a globally exported food product. Echinochrome A (Ech A) is a bioactive compound isolated from the waste product of kina shells and spines; however, the molecular mechanisms of Ech A bioactivity are not well understood, partly due to Ech A never being studied using unbiased genome‐wide analysis. To explore the high‐value pharmaceutical potential of kina food waste, we obtained unbiased functional genomic and proteomic profiles of yeast cells treated with Echinochrome A. Abundance was measured for 4100 proteins every 30 min for four hours using fluorescent microscopy, resulting in the identification of 92 proteins with significant alterations in protein abundance caused by Ech A treatment that were over‐represented with specific changes in DNA replication, repair and RNA binding after 30 min, followed by specific changes in the metabolism of metal ions (specifically iron and copper) from 60–240 min. Further analysis indicated that Ech A chelated iron, and that iron supplementation negated the growth inhibition caused by Ech A. Via a growth‐based genome‐wide analysis of 4800 gene deletion strains, 20 gene deletion strains were sensitive to Ech A in an iron‐dependent manner. These genes were over‐represented in the cellular response to oxidative stress, suggesting that Ech A suppressed growth inhibition caused by oxidative stress. Unexpectedly, genes integral to cardiolipin and inositol phosphate biosynthesis were required for Ech A bioactivity. Overall, these results identify genes, proteins, and cellular processes mediating the bioactivity of Ech A. Moreover, we demonstrate unbiased genomic and proteomic methodology that will be useful for characterizing bioactive compounds in food and food waste. [ABSTRACT FROM AUTHOR]

Feeding and eating disorders (FEDs) are common and have been shown to be influenced by both genetic and environmental factors. Avoidant/restrictive food intake disorder, anorexia nervosa (AN), bulimia nervosa (BN), and binge-eating disorder (BED) are all heritable and genome-wide association studies (GWASs) reveal both psychiatric and metabolic/anthropometric genetic risk factors for AN. GWASs for other FEDs are underway. AN, BN, and BED might diverge etiologically in their genetic relation with metabolic and anthropometric traits. Functional genomic tools will enable translation of variants to genes, genes to pathways, and pathways to metabolic outcomes to convert genetic findings into medically actionable outcomes. This work is poised to yield the first interventions for FEDs that are informed by disorder-specific biology. Feeding and eating disorders (FEDs) are heterogenous and characterized by varying patterns of dysregulated eating and weight. Genome-wide association studies (GWASs) are clarifying their underlying biology and their genetic relationship to other psychiatric and metabolic/anthropometric traits. Genetic research on anorexia nervosa (AN) has identified eight significant loci and uncovered genetic correlations implicating both psychiatric and metabolic/anthropometric risk factors. Careful explication of these metabolic contributors may be key to developing effective and enduring treatments for devastating, life-altering, and frequently lethal illnesses. We discuss clinical phenomenology, genomics, phenomics, intestinal microbiota, and functional genomics and propose a path that translates variants to genes, genes to pathways, and pathways to metabolic outcomes to advance the science and eventually treatment of FEDs. [ABSTRACT FROM AUTHOR]

ChinaMu is the largest sequence‐indexed Mutator (Mu) transposon insertional library in maize (Zea mays). In this study, we made significant improvements to the size and quality of the ChinaMu library. We developed a new Mu‐tag isolation method Mu‐Tn5‐seq (MuT‐seq). Compared to the previous method used by ChinaMu, MuT‐seq recovered 1/3 more germinal insertions, while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time. Using MuT‐seq, we identified 113,879 germinal insertions from 3,168 Mu‐active F1 families. We also assembled a high‐quality genome for the Mu‐active line Mu‐starter, which harbors the initial active MuDR element and was used as the pollen donor for the mutation population. Using the Mu‐starter genome, we recovered 33,662 (15.6%) additional germinal insertions in 3,244 (7.4%) genes in the Mu‐starter line. The Mu‐starter genome also improved the assignment of 117,689 (54.5%) germinal insertions. The newly upgraded ChinaMu dataset currently contains 215,889 high‐quality germinal insertions. These insertions cover 32,224 pan‐genes in the Mu‐starter and B73Ref5 genomes, including 23,006 (80.4%) core genes shared by the two genomes. As a test model, we investigated Mu insertions in the pentatricopeptide repeat (PPR) superfamily, discovering insertions for 92% (449/487) of PPR genes in ChinaMu, demonstrating the usefulness of ChinaMu as a functional genomics resource for maize. [ABSTRACT FROM AUTHOR]

Glypicans are linked to various aspects of neoplastic behavior, and their therapeutic value has been proposed in different cancers. Here, we have systematically assessed the impact of GPC4 on cancer progression through functional genomics and transcriptomic analyses across a broad range of cancers. Survival analysis using TCGA cancer patient data reveals divergent effects of GPC4 expression across various cancer types, revealing elevated GPC4 expression levels to be associated with both poor and favorable prognoses in a cancer-dependent manner. Detailed investigation of the role of GPC4 in glioblastoma and non-small cell lung adenocarcinoma by genetic perturbation studies displays opposing effects on these cancers, where the knockout of GPC4 with CRISPR/Cas9 attenuated proliferation of glioblastoma and augmented proliferation of lung adenocarcinoma cells and the overexpression of GPC4 exhibited a significant and opposite effect. Further, the overexpression of GPC4 in GPC4-knocked-down glioblastoma cells restored the proliferation, indicating its mitogenic effect in this cancer type. Additionally, a survival analysis of TCGA patient data substantiated these findings, revealing an association between elevated levels of GPC4 and a poor prognosis in glioblastoma, while indicating a favorable outcome in lung carcinoma patients. Finally, through transcriptomic analysis, we attempted to assign mechanisms of action to GPC4, as we find it implicated in cell cycle control and survival core pathways. The analysis revealed upregulation of oncogenes, including FGF5, TGF-β superfamily members, and ITGA-5 in glioblastoma, which were downregulated in lung adenocarcinoma patients. Our findings illuminate the pleiotropic effect of GPC4 in cancer, underscoring its potential as a putative prognostic biomarker and indicating its therapeutic implications in a cancer type dependent manner. [ABSTRACT FROM AUTHOR]

Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in the Indian Himalayan Region. It is widely used in medicines, healthcare systems, cosmetics, fodder, and ornamental purposes. The Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers. A total of 18 226 simple sequence repeats (SSRs) were identified wherein di-nucleotides were found to be abundant (47.88%), followed by mono-nucleotide (35.03%) and tri-nucleotide (15.88%) repeats. A total of 11 839 EST-SSR primers were designed, of which 96 primer pairs were commercially synthesized. Finally, 17 primer pairs revealed clear, distinct polymorphic bands, and these primers were validated with 40 diverse B. ciliata accessions. The present study revealed moderate level of genetic diversity (Ho = 0.389, He = 0.542, and PIC = 0.513). Furthermore, the transcriptome data and EST-SSR markers generated during the present investigation could be an important genetic resource for functional genomics, population studies, and conservation genetics of the genus Bergenia. [ABSTRACT FROM AUTHOR]

Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt‐loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme‐coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB‐dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild‐type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose‐dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii. [ABSTRACT FROM AUTHOR]

Apicomplexan parasites are aetiological agents of numerous diseases in humans and livestock. Functional genomics studies in these parasites enable the identification of biological mechanisms and protein functions that can be targeted for therapeutic intervention. Recent improvements in forward genetics and whole‐genome screens utilising CRISPR/Cas technology have revolutionised the functional analysis of genes during Apicomplexan infection of host cells. Here, we highlight key discoveries from CRISPR/Cas9 screens in Apicomplexa or their infected host cells and discuss remaining challenges to maximise this technology that may help answer fundamental questions about parasite–host interactions. [ABSTRACT FROM AUTHOR]

Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species. [ABSTRACT FROM AUTHOR]

This article explores the effects of different oral antidiabetic drugs (OADs) on the gut microbiota in patients with type 2 diabetes (T2D). The study found that acarbose and berberine had significant impacts on the gut microbiota, while metformin, vildagliptin, and glipizide did not. The baseline gut microbiota was found to be associated with the response to OAD treatment. However, the study acknowledges that there are variations in the reported gut microbial alterations due to factors such as ethnicity, sample size, and methodology. Further research is needed to fully understand the interactions between OADs and the gut microbiota and their potential impact on drug efficacy. [Extracted from the article]

Summary: The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross‐scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science. [ABSTRACT FROM AUTHOR]

Capilloviruses represents an important genus of the family Betaflexiviridae and are plant infecting pathogens. They include several agriculturally important viruses encompassing RNA genomes. Apple stem grooving virus (ASGV) is an important virus of this genus. In recent years, reports are accumulating about its expanding host range breadth (HRB) to affect various other plant species. Increased multiple host adaptability of ASGV could be associated with factors like genetic variability, recombination, genome expression strategy, virus transmission and infection biology. The evolution in the viral genome is driving this virus to increased genome variability resulting in infection of different hosts. This review article focuses on recent advances made in understanding ASGV genome biology and possible disease mechanism that may help unravel the complexities of this viral infection conferring multiple host adaptability. Contrarily, this virus also has an immense potential to be used as vector to unveil viral pathogenicity mechanism, its use as Virus Induced Gene Silencing (VIGS)/Virus-Induced Genome Editing (VIGE) vector, and for the enhancement of plant resistance. These features may allow deciphering functional genomics of important crops, enhancement of plant disease resistance ability, ultimately benefiting agriculture, has also been discussed. [ABSTRACT FROM AUTHOR]

The advent of CRISPR/Cas9 technology has revolutionized genome editing, enabling the attainment of once-unimaginable goals. CRISPR/Cas's groundbreaking attributes lie in its simplicity, versatility, universality, and independence from customized DNA-protein systems, erasing the need for specialized expertise and broadening its scope of applications. It is therefore more and more used for genome modification including the generation of mutants. Beyond such editing scopes, the recent development of novel or modified Cas-based systems has spawned an array of additional biotechnological tools, empowering both fundamental and applied research. Precisely targeting DNA or RNA sequences, the CRISPR/Cas system has been harnessed in fields as diverse as gene regulation, deepening insights into gene expression, epigenetic changes, genome spatial organization, and chromatin dynamics. Furthermore, it aids in genome imaging and sequencing, as well as effective identification and countering of viral pathogens in plants and animals. All in all, the non-editing aspect of CRISPR/Cas exhibits tremendous potential across diverse domains, including diagnostics, biotechnology, and fundamental research. This article reviews and critically evaluates the primary CRISPR/Cas-based tools developed for plants and animals, underlining their transformative impact. [ABSTRACT FROM AUTHOR]

Background: The DNA damage response (DDR) is a physiological network preventing malignant transformation, e.g. by halting cell cycle progression upon DNA damage detection and promoting DNA repair. Glioblastoma are incurable primary tumors of the nervous system and DDR dysregulation contributes to acquired treatment resistance. Therefore, DDR targeting is a promising therapeutic anti-glioma strategy. Here, we investigated Ataxia telangiectasia and Rad3 related (ATR) inhibition (ATRi) and functionally-instructed combination therapies involving ATRi in experimental glioma. Methods: We used acute cytotoxicity to identify treatment efficacy as well as RNAseq and DigiWest protein profiling to characterize ATRi-induced modulations within the molecular network in glioma cells. Genome-wide CRISPR/Cas9 functional genomic screens and subsequent validation with functionally-instructed compounds and selected shRNA-based silencing were employed to discover and investigate molecular targets modifying response to ATRi in glioma cell lines in vitro, in primary cultures ex vivo and in zebrafish and murine models in vivo. Results: ATRi monotherapy displays anti-glioma efficacy in vitro and ex vivo and modulates the molecular network. We discovered molecular targets by genome-wide CRISPR/Cas9 loss-of-function and activation screens that enhance therapeutic ATRi effects. We validated selected druggable targets by a customized drug library and functional assays in vitro, ex vivo and in vivo. Conclusion: In conclusion, our study leads to the identification of novel combination therapies involving ATRi that could inform future preclinical studies and early phase clinical trials. [ABSTRACT FROM AUTHOR]

Background: There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.1), type 2 EBNA2 shares only ~ 50% amino acid identity with type 1 and thus may have distinct binding partners, human genome binding locations, and functions. Results: In this study, we examined genome-wide EBNA2 binding in EBV-1 and EBV-2 transformed human B cells to identify shared and unique EBNA2 interactions with the human genome, revealing thousands of type-specific EBNA2 ChIP-seq peaks. Computational predictions based on hTF motifs and subsequent ChIP-seq experiments revealed that both type 1 and 2 EBNA2 co-occupy the genome with SPI1 and AP-1 (BATF and JUNB) hTFs. However, type 1 EBNA2 showed preferential co-occupancy with EBF1, and type 2 EBNA2 preferred RBPJ. These differences in hTF co-occupancy revealed possible mechanisms underlying type-specific gene expression of known EBNA2 human target genes: MYC (shared), CXCR7 (type 1 specific), and CD21 (type 2 specific). Both type 1 and 2 EBNA2 binding events were enriched at systemic lupus erythematosus (SLE) and multiple sclerosis (MS) risk loci, while primary biliary cholangitis (PBC) risk loci were specifically enriched for type 2 peaks. Conclusions: This study reveals extensive type-specific EBNA2 interactions with the human genome, possible differences in EBNA2 interaction partners, and a possible new role for type 2 EBNA2 in autoimmune disorders. Our results highlight the importance of considering EBV type in the control of human gene expression and disease-related investigations. [ABSTRACT FROM AUTHOR]

The members of MADS-box gene family have important roles in regulating the growth and development of plants. MADS-box genes are highly regarded for their potential to enhance grain yield and quality under shifting global conditions. Wild emmer wheat (Triticum turgidum subsp. dicoccoides) is a progenitor of common wheat and harbors valuable traits for wheat improvement. Here, a total of 117 MADS-box genes were identified in the wild emmer wheat genome and classified to 90 MIKCC, 3 MIKC*, and 24 M-type. Furthermore, a phylogenetic analysis and expression profiling of the emmer wheat MADS-box gene family was presented. Although some MADS-box genes belonging to SOC1, SEP1, AGL17, and FLC groups have been expanded in wild emmer wheat, the number of MIKC-type MADS-box genes per subgenome is similar to that of rice and Arabidopsis. On the other hand, M-type genes of wild emmer wheat is less frequent than that of Arabidopsis. Gene expression patterns over different tissues and developmental stages agreed with the subfamily classification of MADS-box genes and was similar to common wheat and rice, indicating their conserved functionality. Some TdMADS-box genes are also differentially expressed under drought stress. The promoter region of each of the TdMADS-box genes harbored 6 to 48 responsive elements, mainly related to light, however hormone, drought, and low-temperature related cis-acting elements were also present. In conclusion, the results provide detailed information about the MADS-box genes of wild emmer wheat. The present work could be useful in the functional genomics efforts toward breeding for agronomically important traits in T. dicoccoides. [ABSTRACT FROM AUTHOR]

Summary Deep neural networks (DNNs) have been widely applied to predict the molecular functions of the non-coding genome. DNNs are data hungry and thus require many training examples to fit data well. However, functional genomics experiments typically generate limited amounts of data, constrained by the activity levels of the molecular function under study inside the cell. Recently, EvoAug was introduced to train a genomic DNN with evolution-inspired augmentations. EvoAug-trained DNNs have demonstrated improved generalization and interpretability with attribution analysis. However, EvoAug only supports PyTorch-based models, which limits its applications to a broad class of genomic DNNs based in TensorFlow. Here, we extend EvoAug's functionality to TensorFlow in a new package, we call EvoAug-TF. Through a systematic benchmark, we find that EvoAug-TF yields comparable performance with the original EvoAug package. Availability and implementation EvoAug-TF is freely available for users and is distributed under an open-source MIT license. Researchers can access the open-source code on GitHub (https://github.com/p-koo/evoaug-tf). The pre-compiled package is provided via PyPI (https://pypi.org/project/evoaug-tf) with in-depth documentation on ReadTheDocs (https://evoaug-tf.readthedocs.io). The scripts for reproducing the results are available at (https://github.com/p-koo/evoaug-tf_analysis). [ABSTRACT FROM AUTHOR]

We performed a functional analysis of two potential partners of ASF1, a highly conserved histone chaperone that plays a crucial role in the sexual development and DNA damage resistance in the ascomycete Sordaria macrospora. ASF1 is known to be involved in nucleosome assembly and disassembly, binding histones H3 and H4 during transcription, replication and DNA repair and has direct and indirect roles in histone recycling and modification as well as DNA methylation, acting as a chromatin modifier hub for a large network of chromatin-associated proteins. Here, we functionally characterized two of these proteins, RTT109 and CHK2. RTT109 is a fungal-specific histone acetyltransferase, while CHK2 is an ortholog to PRD-4, a checkpoint kinase of Neurospora crassa that performs similar cell cycle checkpoint functions as yeast RAD53. Through the generation and characterization of deletion mutants, we discovered striking similarities between RTT109 and ASF1 in terms of their contributions to sexual development, histone acetylation, and protection against DNA damage. Phenotypic observations revealed a developmental arrest at the same stage in Δrtt109 and Δasf1 strains, accompanied by a loss of H3K56 acetylation, as detected by western blot analysis. Deletion mutants of rtt109 and asf1 are sensitive to the DNA damaging agent methyl methanesulfonate, but not hydroxyurea. In contrast, chk2 mutants are fertile and resistant to methyl methanesulfonate, but not hydroxyurea. Our findings suggest a close functional association between ASF1 and RTT109 in the context of development, histone modification, and DNA damage response, while indicating a role for CHK2 in separate pathways of the DNA damage response. [ABSTRACT FROM AUTHOR]

Brassica napus, commonly known as rapeseed or canola, is a major oil crop contributing over 13% to the stable supply of edible vegetable oil worldwide. Identification and understanding the gene functions in the B. napus genome is crucial for genomic breeding. A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B. napus. In this review, we present an overview of the progress made in the functional genomics of B. napus, including the availability of germplasm resources, omics databases and cloned functional genes. Based on the current progress, we also highlight the main challenges and perspectives in this field. The advances in the functional genomics of B. napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B. napus and will expedite the breeding of high quality, high resistance and high yield in B. napus varieties. [ABSTRACT FROM AUTHOR]

Most SNPs associated with complex diseases seem to lie in non-coding regions of the genome; however, their contribution to gene expression and disease phenotype remains poorly understood. Here, we established a workflow to provide assistance in prioritising the functional relevance of non-coding SNPs of candidate genes as susceptibility loci in polygenic neurological disorders. To illustrate the applicability of our workflow, we considered the multifactorial disorder migraine as a model to follow our step-by-step approach. We annotated the overlap of selected SNPs with regulatory elements and assessed their potential impact on gene expression based on publicly available prediction algorithms and functional genomics information. Some migraine risk loci have been hypothesised to reside in non-coding regions and to be implicated in the neurotransmission pathway. In this study, we used a set of 22 non-coding SNPs from neurotransmission and synaptic machinery-related genes previously suggested to be involved in migraine susceptibility based on our candidate gene association studies. After prioritising these SNPs, we focused on non-reported ones that demonstrated high regulatory potential: (1) VAMP2 _rs1150 (3′ UTR) was predicted as a target of hsa-mir-5010-3p miRNA, possibly disrupting its own gene expression; (2) STX1A _rs6951030 (proximal enhancer) may affect the binding affinity of zinc-finger transcription factors (namely ZNF423) and disturb TBL2 gene expression; and (3) SNAP25 _rs2327264 (distal enhancer) expected to be in a binding site of ONECUT2 transcription factor. This study demonstrated the applicability of our practical workflow to facilitate the prioritisation of potentially relevant non-coding SNPs and predict their functional impact in multifactorial neurological diseases. [ABSTRACT FROM AUTHOR]

A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1–4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation. Improved coverage of super-resolution Ribo-seq in Arabidopsis reveals uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. [ABSTRACT FROM AUTHOR]