🧬 Category

genomics

407 papers

Comparative genomics reveals signatures of distinct metabolic strategies and gene loss associated with Hydra immortality

This study presents a high-quality genome assembly of the immortal *Hydra vulgaris* and reveals that its longevity is associated with distinct metabolic signatures and the paradoxical loss of canonical anti-aging genes, rather than their presence, suggesting that immortality arises from unique metabolic organization and epigenetic stability rather than simply accumulating longevity factors.

Nojiri, K., Kin, K., Someya, A. + 5 more2026-03-07🧬 genomics

Exploring genetic, expression and regulatory patterns of parental alleles in Muscovy duck (Cairina moschata) using haplotype-resolved assemblies

This study utilizes high-quality haplotype-resolved assemblies of Muscovy ducks to characterize parental allele patterns in the female-heterogametic ZW system, revealing distinct maternal-biased chromatin accessibility and expression alongside Z-chromosome dosage compensation mechanisms that advance the understanding of heterosis in poultry.

Li, T., Wang, y., Zhang, Z. + 7 more2026-03-07🧬 genomics

The complete chloroplast genome of Garcinia binucao (Blanco) Choisy, an indigenous fruit from the Philippines

This study presents the first complete chloroplast genome of the indigenous Philippine fruit *Garcinia binucao*, detailing its 156,570 bp quadripartite structure, 128 annotated genes, and phylogenetic relationship to *G. indica* to establish a foundational genomic resource for future conservation and utilization efforts.

Cacao, M. A., Munoz, J. A. M., Coronado, J. E. + 6 more2026-03-07🧬 genomics

Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance

This study presents seven high-quality reference genomes for side-necked turtles, revealing that rare chromosomal bursts drove karyotype diversity, genetic sex determination in Chelidae originated over 80 million years ago on a microchromosome, and specific gene losses coupled with adaptive changes underpin the turtles' unique skeletal structure, longevity, and cancer resistance.

Hilgers, L., Rovatsos, M., Kontopoulos, D. - G. + 15 more2026-03-07🧬 genomics

Diversity and Genomic Organization of Non-B DNA Motifs in Haplotype-Resolved Human Genome Assemblies

This study leverages 130 haplotype-resolved long-read genome assemblies to systematically characterize the diversity, stability, and genomic distribution of non-B DNA motifs across diverse human populations, revealing significant population-level variation and their specific enrichment in previously inaccessible, evolutionarily dynamic regions such as centromeres and segmental duplications.

Turco, A., Boev, N., Kumar, S.2026-03-07🧬 genomics

A Translocation within the Ogataea Species Complex Alters Local Subtelomeric Chromatin while Maintaining Overall Genome Organization

This study demonstrates that while closely related *Ogataea* yeast species maintain conserved global genome organization and histone modification patterns, a specific chromosomal translocation in *O. haglerorum* significantly alters local subtelomeric chromatin composition and gene expression, highlighting microevolutionary impacts on genome function.

Lundberg, T. J., Lande, N. M., Tourevski, D. + 3 more2026-03-07🧬 genomics

Alternative 3' Polyadenylation Responses to Acute Ethanol Exposure Differ Between Drosophila Populations

This study reveals that acute ethanol exposure triggers widespread but genetically contingent alternative polyadenylation in *Drosophila melanogaster*, where cosmopolitan French populations predominantly exhibit 3' UTR shortening while ancestral Zambian populations show 3' UTR lengthening, highlighting population-specific APA remodeling as a key molecular mechanism underlying adaptive responses to environmental stress.

Boateng-Sarfo, G., Lee, S., Lai, E. C. + 1 more2026-03-07🧬 genomics

MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

The authors developed MERFISH 2.0, an optimized spatial transcriptomics chemistry that significantly enhances transcript detection sensitivity (up to ~8-fold) in degraded and archival tissues like FFPE samples compared to its predecessor, thereby enabling robust, scalable, and high-resolution spatial analysis across diverse clinically relevant specimens.

He, L., Wang, B., Wiggin, T. + 19 more2026-03-07🧬 genomics

A Zero-Inflated Hierarchical Generalized Transformation Model to Address Non-Normality in Spatially-Informed Cell-Type Deconvolution

This paper introduces a novel zero-inflated hierarchical generalized transformation model (ZI-HGT) integrated with the CARD framework to improve the accuracy and uncertainty quantification of cell-type deconvolution in spatially-informed oral squamous cell carcinoma data by addressing high zero-inflation and non-normality, thereby enabling the precise localization of fibroblast populations within the tumor microenvironment.

Melton, H. J., Bradley, J. R., Wu, C.2026-03-06🧬 genomics

Decontaminating genomic data for accurate species delineation and hybrid detection in the Lasius ant genus

This study demonstrates that implementing a specific decontamination pipeline on a RADseq dataset of over 1,000 *Lasius* ants eliminates false signals of widespread hybridization, revealing that introgression in this genus is actually extremely rare and underscoring the critical need for systematic contamination checks in genomic research.

Jecha, K., Lavanchy, G., Schwander, T.2026-03-06🧬 genomics

Using pangenome variation graphs to improve mutation detection in a large DNA virus

This study demonstrates that constructing compact pangenome variation graphs from representative lumpy skin disease virus (LSDV) lineages significantly outperforms traditional linear reference mapping by reducing reference bias, recovering previously undetected mutations in immune-related genes, and enhancing genomic surveillance for large DNA viruses.

Downing, T., Tennakoon, C., Lasecka-Dykes, L. + 1 more2026-03-06🧬 genomics

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs

By integrating ribosome profiling and Nanopore direct RNA sequencing across multiple *Saccharomyces* species, this study identifies thousands of translated upstream ORFs in yeast that encode conserved, functional microproteins under purifying selection, while demonstrating that downstream ORFs are largely non-conserved and less likely to be functional.

Montanes, J. C., Papadopoulos, C., Al-Obaidi, S. + 6 more2026-03-06🧬 genomics

Defining a tandem repeat catalog and variation clusters for genome-wide analyses

This paper introduces the TRExplorer catalog v1.0, a comprehensive, 4.86-million-locus tandem repeat resource designed for both short- and long-read analyses that resolves inconsistencies in existing catalogs by defining variation clusters through a novel algorithm, thereby enabling more accurate genome-wide genotyping and facilitating a unified portal for data access.

Weisburd, B., Dolzhenko, E., Bennett, M. F. + 20 more2026-03-05🧬 genomics