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Haplotype-resolved genomes

Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade, we show that despite genome size reduction during evolution, these bivalves maintain remarkable genetic variability. By constructing a haplotype-resolved genome for Crassostrea sikamea, we identify widespread haplotype divergent sequences (HDSs), representing genomic regions unique to each haplotype. We show that HDSs are driven by transposable elements, playing a key role in creating and maintaining genetic diversity during oyster evolution. Comparisons of haplotype-resolved genomes across four bivalve orders uncover diverse HDS origins, highlighting a role in genetic innovation ...
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Disease

Diseases of Genetics and Genomics  A disease is a particular abnormal condition that adversely affects the structure or function of all or part of an organism and is not immediately due to any external injury.[1] Diseases are often known to be medical conditions that are associated with specific signs and symptoms. A disease may be caused by external factors such as pathogens or by internal dysfunctions. For example, internal dysfunctions of the immune system can produce a variety of different diseases, including various forms of immunodeficiency, hypersensitivity, allergies, and autoimmune disorders. In humans, disease is often used more broadly to refer to any condition that causes pain, dysfunction, distress, social problems, or death to the person affected, or similar problems for those in contact with the person. In this broader sense, it sometimes includes injuries, disabilities, disorders, syndromes, infections, isolated symptoms, deviant behaviors, and atypical variations ...
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Genetic Diversity Analysis

Nutritional quality evaluation and genetic diversity analysis of walnut nuts Walnut (Juglans regia L.) trees have been seed-propagated for over a thousand years in Tibet, thriving under variable climatic conditions at altitudes exceeding 3,000 m. This study conducted a comprehensive evaluation of the nutritional quality of 175 walnuts, identifying the highest-performing accessions. Additionally, 20 simple sequence repeat (SSR) loci were employed to assess the extent of genetic diversity and the genetic relationships among the walnuts. The walnut JC174, JC170, and JC126 were ranked among the top three based on a comprehensive evaluation using principal component analysis. A total of 319 alleles were identified, and seven highly polymorphic loci, including SSR6, were selected for further study. The genetic diversity analysis indicated that the majority of genetic variation in Jiacha walnuts was observed among individuals, leading to the division of the population into two distinct group...
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Genetic variants in Tumors

Using AI to identify genetic variants in tumors with DeepSomatic DeepSomatic is an AI-powered tool that identifies cancer-related mutations in a tumor’s genetic sequence to help pinpoint what’s driving the cancer. Cancer is fundamentally a genetic disease in which the genetic controls on cell division go awry. Many types of cancer exist, and each poses unique challenges as it can have distinct genetic underpinnings. A powerful way to study cancer, and a critical step toward creating a treatment plan, is to identify the genetic mutations in tumor cells. Indeed, clinicians will now often sequence the genomes of biopsied tumor cells to inform treatment plans that specifically disrupt how that cancer grows. With partners at the University of California, Santa Cruz Genomics Institute and other federal and academic researchers, our new paper, “DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies” in Nature Biotechnology presents a tool that leverages m...
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Characterization of miRNAs

Transcriptomic Characterization of miRNAs in Pyrrhalta aenescens Fairmaire in Response to 20-Hydroxyecdysone Treatment Pyrrhalta aenescens, a major pest of elm trees, causes extensive ecological and economic damage through rapid population growth and defoliation. Existing research mainly focuses on its biological traits and chemical control, with little knowledge about its reproductive development mechanisms, a key factor in population expansion. In other insects, the steroid hormone 20-hydroxyecdysone (20E) regulates development and reproduction via microRNA (miRNA)-mediated pathways, but this has not been studied in P. aenescens. This study aimed to systematically identify miRNAs responsive to 20E in P. aenescens and unravel their roles in regulating reproduction and metabolic pathways, providing foundational insights into hormone–miRNA crosstalk in this ecologically significant pest. Adult beetles (collected from Baotou, Inner Mongolia) were injected with 1.0 μg/μL 20E or control. ...
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Genetic Dissection

Genetic Dissection of Yield-Related Traits in a Set of Maize Recombinant Inbred Lines Under Multiple Environments Agronomic advancements have led to significant increases in maize yield per hectare in Northeast China, primarily through improved density tolerance. However, the genetic mechanism underlying grain yield responses to density stress remains poorly understood. Here, a population of 193 recombinant inbred lines (RILs) derived from the cross between ZM058 and PH1219 was employed to identify quantitative trait loci (QTLs) under two planting densities across three locations over two years. Six yield-related traits were investigated: ear tip-barrenness length (BEL), cob diameter (CD), ear diameter (ED), ear length (EL), kernel number per row (KNR), and kernel row number (KRN).  These traits exhibited distinct and divergent responses to density stress, with the values of CD, ED, EL, KNR and KRN decreasing as planting density increased, except for BEL. A total of 81 QTLs were id...
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Genetic deletion in cerebellum

Genetic deletion in cerebellum impedes hemisphere formation, study finds The cerebellum, a brain region located at the back of the head that has long been known to support the coordination of muscle movements, has recently also been implicated in more sophisticated mental functions. Purkinje cells are the only neurons located in the cerebellum that integrate information in the cerebellar cortex and send it to other parts of the nervous system. Purkinje cells are large and highly branched nerve cells that can have different functions. While many past studies have explored the roles of these cells, the neural and genetic processes shaping their diversity have not yet been fully elucidated. Researchers at the University of Connecticut School of Medicine recently carried out a study aimed at exploring the possible role of the FOXP genes, a family of genes known to contribute to switching other genes "on and off," in shaping Purkinje cell populations and the formation of circuits...
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