Search

High yield and wide adaptation rice are crucial for grain supply and food security. Here the authors report OsPI4Kγ7 which contributes to different “adaptability-yield” trade-offs in japonica and indica, and provides an alternative breeding strategy for raising grain yield in different latitudes.

Structural variants are an underexplored source of genetic diversity. Here, the authors use phased pangenome graphs to improve detection of these variants in dairy cattle and link these variants to traits of economic importance.

The changing cellular, transcriptional, and genomic landscape of human lung aging can be characterized using single-cell RNA sequencing. Here, the authors show that lung aging is cell-type dyssynchronous, with alveolar epithelial and endothelial cells exhibiting the greatest changes in gene expression, transcriptional entropy, and a high level of somatic mutations.

Genome evolutionary history of wild Arachis species remains unclear. Here, the authors report the origin of small chromosome A08 and genome evolution of Arachis species via comparative oligopainting and genomic analysis of A. hoehnei.

Here the authors systematically benchmark 13 polygenic score (PGS) methods in UK Biobank European and African populations, revealing factors that affect prediction accuracy. They also introduce an automated platform for standardized and reproducible PGS computation.

Papaya is a trioecious species with XX females, XY males, and XY^h hermaphrodites, and the combination of Y and Y^h chromosomes is lethal. Here, the authors identify the degeneration of the YY lethality gene on the Y chromosome as the causal balancing lethal factor that reenforces dioecy and stabilizes balanced sex ratios.

Large-effect variants in autism remain elusive. Here, the authors use long-read sequencing to assemble phased genomes for 189 individuals, identifying pathogenic variants in TBL1XR1, MECP2, and SYNGAP1, plus nine candidate structural variants missed by short-read methods.

Current mapping of fork progression in the human genome suffers from drastically low throughput. Here, the authors introduce ForkML, a nanopore sequencing-based method automatically positioning thousands of individual fork velocities by tracking BrdU incorporation into asynchronously growing cells.

RNA modifications influence gene regulation, but global mapping was limited. Here, the authors introduce ORCA, a deep learning framework using nanopore RNA sequencing to detect multiple modification types, revealing isoform-specific patterns and regulatory interactions.

Via an integrative modelling approach that combines population and clinical trial data, the authors find that polygenic risk score-based screening would reduce premature mortality across seven commonly screened conditions.

Natural variation in the promoter of OsTPS8 contributes to differences in grain chalkiness and seed vigor between indica and japonica rice subspecies by altering trehalose-6-phosphate biosynthesis and α-amylase levels.

In maize, ZmDapF1 suppresses the activity of ZmMDH6 in chloroplasts, exacerbating oxidative damage under drought. Knocking out ZmDapF1 or using its favourable allele with lower gene expression enhances drought resilience without yield penalty.

Schizophrenia risk at 1p36.23 lacked functional insight. Here, the authors identify two enhancer variants that upregulate RERE, which disrupts neurogenesis and synaptic function by regulating Grin2a, linking genetic risk to neuronal development and excitatory signaling.

Changes in gene regulation are a major driver of human traits and disease. Here, authors develop e2MPRA, a high-throughput technology that simultaneously measures enhancer activity and associated epigenetic modifications, revealing how sequence variants influence regulatory function.

The links between meat production and immunity in cattle can affect agricultural production. Here, Li et al. identify genetic and environmental factors that shape immune responses in cattle, which can guide breeding for improved health.

This study shows that promoter and enhancer functions are often linked within the same DNA sequences. Using a dual-reporter assay, the authors reveal shared sequence features and co-dependent activities supporting a unified model of gene regulation.

The factors contributing to the onset of Barrett’s esophagus, a precancerous stage of the highly lethal esophageal cancer, remain elusive. Here, the authors identify inherited mutations in the VSIG10L gene as a key etiologic determinant affecting esophageal biology and facilitating the development of Barrett’s esophagus.

For proper mitochondrial inheritance, paternal sperm mitochondria must be eliminated. Here, authors identify ALKB-1 mediated tRNA demethylation as essential for this clearance in Caenorhabditis elegans, revealing an epitranscriptomic quality checkpoint tied to male fertility.

MraZ, a conserved transcription factor, controls bacterial cell division by binding the dcw operon promoter. Here, the authors present cryo-EM structures of M.genitalium MraZ with its 4-box promoter, revealing its DNA-binding mechanism

Dimorphic organisms switch between two distinct life forms, but how a single genome controls the genetic program for both states is unclear. The study identifies hundreds of convergently evolved gene families and two regulator genes, dkl and dfl, that coordinate expression to optimize the two morphologies of Mucorales fungi.

This study demonstrates that the Drosophila proventriculus, the structure at the anterior of gut that synthesizes the peritrophic membrane, lacks stem cells but undergoes continual endocycling to compensate for cells loss during aging or damage.

Lactation is essential, but its genetic and epigenetic regulation is poorly understood. Here, Hanin et al. show that ZFP57 has an imprinting-independent role in controlling postnatal nutritional support, expanding its known prenatal epigenetic functions.

Chromatin states need to be maintained during DNA damage repair. Here, the authors expand the histone chaperone network involved in repair-coupled chromatin restoration and highlight a mechanistic coordination between old and new histone dynamics.

Grain number per panicle (GNP) is a yield-determining trait of rice. Here, the authors identify a GSK3-like kinase-encoding gene GNP2 and a bZIP transcription factor-encoding gene GNP5, demonstrating their synergistic regulation of GNP and showing that specific allele combinations of these genes enhance rice yield in field conditions.

This study reports that de novo germline missense variants in SF3B1, distinct from the somatic variants frequently observed in cancer, cause a neurodevelopmental disorder and disrupt global RNA splicing.

Grain chalkiness is an undesirable trait that severely compromises rice quality. Here, the authors report the cloning of an E3 ubiquitin ligase encoding gene Chalk9 and reveal its crucial role in regulating grain chalkiness through mediating the ubiquitination-dependent degradation of OsEBP89.

Pangenomic and epidemiological analyses reveal a genetic shift in U.S. Salmonella Hadar populations during 2019–20, driven by expansion of a lineage carrying a prophage-like element that likely arose in commercial poultry and spread to backyard flocks.

Polygenic scores often underperform in non‑European ancestries. Here, the authors present GPTL, an R package with three transfer‑learning methods that improve cross‑ancestry PGS using either individual‑level data or GWAS summary statistics.

Tea plant has a highly complex and heterozygous genome, and can produce abundant beneficial metabolites. Here, the authors report the haplotype-resolved genome of cultivar Fuding Dabaicha and reveal structural variations associated with secondary metabolism diversity through QTL and mGWAS analyses.

Here, the authors combine bioinformatic, mass spectrometric, and sequencing-based mapping tools to identify previously undescribed phosphorothioate epigenetic systems widespread in the human gut microbiome.

Animals must obtain half of their amino acids from the diet, influencing their evolution and metabolism. This study suggests that energy pressures favored this outsourcing, enabling proteins to evolve more freely and supporting the emergence of animals.

DNA demethylation enzyme TET1 is a known oncogene in leukemia. Here, the authors discover that TET1 is involved in GPX4-dependent and -independent ferroptosis in acute myeloid leukemia via the regulation of GSH synthesis enzyme GCLC and BH4 synthesis enzyme GCH1.

It is not fully understood why genomic loci show asynchronous DNA replication. Here, the authors show that two imprinted gene domains replicate asynchronously between the parental chromosomes due to differential DNA methylation and non-coding RNA, leading to allelic differences.

The role of lipid metabolism in Parkinson's disease is poorly understood. Here, Ren and co-authors identify a key enzyme in this process, mitochondrial glycerol 3-phosphate acyltransferase, as a critical driver of α-synuclein toxicity.

Direct RNA sequencing suffers from chimera artifact contamination. Here, the authors develop DeepChopper, a genomic language model that detects artifacts with high accuracy, enabling more reliable transcriptome analysis.

This study reveals that the ability to maintain a stable body weight predicts longevity in mice. By tracking weight dynamics throughout life, the authors identify genetic loci linked to body weight, energy homeostasis and healthy aging.

Japonica subspecies has a lower nitrogen use efficiency (NUE) than that of indica rice. Here, the authors show that natural variations in the NIN-like protein 4 (OsNLP4) encoding gene are responsible for the divergence and introgression of the indica OsNLP4 allele into elite japonica cultivar can increase NUE and grain yield.

Asexual-to-sexual switching underpins malaria transmission. Prajapati et al. identify an AP2-G loss-of function mutation and use it as a genetic tool to show that GDV1 is essential for initial ap2-g activation and sexual commitment initiation.

Several recent publications have attempted to detect novel unannotated microproteins using mass spectrometry proteomics. Here, the authors reassess these claimed microprotein detections, finding that many are poorly supported, while a subset represents likely genuine discoveries of novel proteins.

EZHIP, an inhibitor of PRC2, is required for female fertility in mice. Here, the authors show that maternal deletion of Ezhip impairs H3K27me3 deposition post-fertilization. This notably translates into the loss of H3K27me3-dependent gene imprinting.

This study applies generalized linear mixed models (GLMM) and advanced transcriptome wide association study (TWAS) methods to improve the discovery of colorectal cancer risk transcription factors and genes, including potential druggable targets.

Genetic predictors of health outcomes often drop in accuracy when applied to people dissimilar to participants of large genetic studies. Here, the authors investigate the root causes and highlight open questions underlying this problem.

The study used snMultiome-seq to map gene expression and chromatin accessibility in human central amygdala cells from people with and without AUD. Here, the authors show that inhibitory neurons are most affected, with KLF16-driven regulatory changes and AUD-risk variants disrupting gene activity.

Life’s transition between saltwater and freshwater environments requires major genetic innovations. This study reveals the key genes for salinity adaptation in Chlorella sp. MEM25, an early saltwater alga.

The mechanism of transitions in sex determination systems are often poorly understood. This study looks at the amphioxus Branchiostoma belcheri, and finds repeated transpositions of the gene tesD have created new sex-determining regions, driving turnover of the sex determination system.

Authors use metagenomic environmental surveillance in Cambodian live-bird markets and found that air sampling captured the greatest diversity of poultry viruses. It outperformed traditional swabs, identifying undetected H5N1 clades.

Haldane’s rule suggests that in hybrid crosses, the heterogametic sex is often rare or sterile. This study crosses Caenorhabditis nematodes, and determines that an underlying feature of Haldane’s rule is incompatibility between a sex chromosome derived from only one species and autosome pairs from both.

Several genes in regulating flowering time have been identified in soybean, but the epigenetic regulators are still largely unknown. Here, the authors identify GmLDL2, a histone H3K4me1/2 demethylase, as a crucial flowering time regulator in soybean.