Research Radar

Single base focal hypermutation cooccurs with structural variation as an early event in advanced prostate tumourigenesis with ancestry specific independence: a multi-ancestral observational study.

Jue Jiang, Avraam Tapinos, Ruotian Huang, et al.

Pangenome-assisted characterization of TaBAM genes and association of TaBAM16-1B with NDVI in wheat.

Maira Anam, Zulqurnain Khan, Muhammad Ali Sher, et al.

Β-amylase (BAM) gene family is an important genetic resource that catalyzes starch metabolism and responds positively in response to abiotic stresses. In current work, 28 TaBAMs were identified through genome wide analysis using AtBAM domain. Phylogenetic analysis grouped these genes into four sub-groups. Gene structure, conserved...

Pathway-level somatic mutation burden reflects diffuse genomic accumulation rather than selective transcriptional disruption in ovarian serous carcinoma: Evidence from bulk, spatial, and multi-region genomic analyses.

Elif Kardelen Çağdaş

Whether increasing tumor mutation burden (TMB) drives selective transcriptional pathway disruption or reflects diffuse genomic accumulation in ovarian serous carcinoma remains unclear. TMB-transcriptome relationships were examined in the CPTAC-GDC cohort (n = 84) using Spearman correlations between continuous TMB and ssGSEA-derived...

Endogenous retroviruses in livestock and poultry: From genomic invaders to beneficial allies.

Ali Shoaib Moawad, Amaal Omara, Tuofan Li, et al.

Endogenous retroviruses (ERVs), the genomic remnants of ancient retroviral infections, constitute a significant and dynamic component of livestock and poultry genomes. This review synthesizes current knowledge on the dual roles of ERVs, from drivers of genomic instability and disease to essential agents of evolution and innovation in...

Machine learning-based prediction of Familial Hemiplegic Migraine risk from genetic variants.

Mohammed M Alfayyadh, Neven Maksemous, Heidi G Sutherland, et al.

Familial Hemiplegic migraine (FHM) is a rare migraine subtype characterised by transient unilateral motor weakness. Although familial forms are associated with variants in CACNA1A, ATP1A2, and SCN1A genes, many cases remain genetically unexplained, suggesting contributions from additional rare variations including single-nucleotide...

Telomere-to-telomere genome assemblies and population resequencing of diploid and allotetraploid peanut varieties.

Jianxin Bian, Yilin Zhang, Shuai Ding, et al.

Peanut (Arachis hypogaea L.) is a globally significant leguminous oil crop. Here we present telomere-to-telomere genome assemblies for two diploid and four tetraploid peanut varieties, resulting in high-quality reference genomes, showing that the complex activities of transposable elements, chromosomal rearrangements and centromere...

Allelic association analyses: estimation recommendations.

Bruce S Weir, Jérôme Goudet

We offer our perspective on the rich literature on the estimation of measures of inbreeding, relatedness, and population structure, beginning with Sewall Wright's F-statistics and moving onto the descriptive statistics of Masatoshi Nei and Clark Cockerham before discussing recent papers. The current availability of genome-level single...

Repurposing Quetiapine as an Adjuvant Therapeutic Agent for Triple-Negative Breast Cancer.

Ling He, Purva Joshi, Angeliki Ioannidis, et al.

Triple-negative breast cancer (TNBC) lacks actionable molecular targets, so treatment primarily relies on cytotoxic chemotherapy and radiotherapy, yet relapse, resistance, and metastasis still drives poor long-term survival. Dopamine signaling has recently been linked to tumor aggressiveness, and dopamine-receptor antagonists have shown...

Genome degradation in plant tissue culture.

Matthew W Davis, Charles A Leslie, Chaehee Lee, et al.

Many plants, unlike most animals, can reproduce as clones [D. Kester, HortScience 18, 831-837 (1983), 10.21273/hortsci.18.6.831]. Cloning plants is vital to agriculture and biotechnology [H. Barton, T. Denham, Quatern. Int. 489, 17-25 (2018), O. L. Gamborg, In Vitro Cell. Dev. Biol. Plant 38, 84-92 (2002), K.-H. Neumann, A. Kumar, J....

Disruption of bacteriophage integration site promotes rapid diversification of multicellular traits in Bacillus subtilis.

Maja Popović, Tomaž Accetto, Yasmine Dergham, et al.

Certain bacteria are known for their remarkable genetic and phenotypic diversity, as well as rapid morphological diversification during evolution experiments. An example is Bacillus subtilis, which can switch motility, biofilm, or antagonistic interaction patterns. Here, we investigated how different forms of disruption at the spsM...

Multiomics Analysis Identifies Chromosomal Instability-Associated Immune-Related Signatures in Hepatocellular Carcinoma by Integrating Weighted Gene Coexpression Network Analysis (WGCNA) and Machine Learning.

Zehao Li, Boqiang Zhong, Qian Zhang, et al.

Hepatocellular carcinoma (HCC) is a top cause of cancer-related death globally, with late diagnosis due to nonspecific early symptoms. Current single-factor prognostic models cannot reflect tumor heterogeneity, so a comprehensive tool for risk stratification and personalized treatment is needed. This study employed WGCNA on publicly...

wavess 1.2: Presenting an HLA-aware within-host virus sequence simulation framework.

Zena Lapp, Thomas Leitner

Understanding how virus sequences are shaped by selection can inform vaccine design and transmission inference. Modeling within-host evolution to interrogate these questions requires a detailed mechanistic framework that accurately captures sequence diversification. The CD8 + cytotoxic T-lymphocyte (CTL) response plays an important role...

Loss of Pol32, a subunit of DNA polymerases δ and ζ, leads to different patterns of genome stability than direct impairment of these individual polymerases.

Lei Qi, Ke-Jing Li, Xing-Xing Tang, et al.

Pol32 is a subunit shared by DNA polymerases δ and ζ, yet its role in maintaining genome integrity remains incompletely defined. Here, we employed whole-genome sequencing of mutation-accumulation lines to systematically characterize the genome-wide effects of a POL32 deletion in diploid Saccharomyces cerevisiae. Loss of Pol32 led to...

The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.

Olivier Arnaiz, Frédéric Guérin, Arnaud Couloux, et al.

Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual generations. A polyploid transcriptionally active somatic macronucleus (MAC) develops at each sexual generation from a copy of the MIC through programmed...

Metabolic-renal disease genetic architecture revealed by genomic structural equation modeling.

Kaixi Ding, Li Xiang, Wei Jiang, et al.

Physiologic mechanisms underlying metabolic and renal diseases interact and are highly comorbid, yet their genetic associations and underlying mechanisms have not been systematically elucidated. Using genome-wide association study (GWAS) summary statistics from UK Biobank, FinnGen, and CKDGen, we integrated and analyzed gout, serum...

GC content variation in angiosperm genomes reveals GC-biased gene conversion.

Qing Xian, Liu Yang, Yuan Wang, et al.

This study reveals the diversity of GC content characteristics among major angiosperm groups, with Poaceae species exhibiting significantly higher GC content and more pronounced heterogeneity. These features are likely associated with GC-biased gene conversion. Genome nucleotide composition critically shapes plant genetic diversity, yet...

Coalescence and translation: A language model for population genetics.

Kevin Korfmann, Nathaniel S Pope, Melinda Meleghy, et al.

Probabilistic models such as the sequentially Markovian coalescent have long provided a powerful framework for population genetic inference, enabling reconstruction of demographic history and ancestral relationships from genomic data. However, these methods are inherently specialized, relying on predefined assumptions and/or limited...

Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity.

Yaen Chen, Keila Velazquez-Arcelay, John A Capra

Statistical methods to identify Neanderthal ancestry in modern human genomes rest on varying assumptions and inputs. Nonetheless, most studies of introgression use only a single method to define Neanderthal ancestry. Due to a lack of "ground truth," we have a limited understanding of the accuracy, comparative strengths and weaknesses,...

Recovering signatures of archaic introgression using ancestral recombination graphs.

Yulin Zhang, Arjun Biddanda, Sarah A Johnson, et al.

Neanderthal and Denisovan genomes have reshaped our understanding of archaic introgression. Yet, the limited number of archaic genomes sequenced and the reliance on unadmixed outgroups have left much of this history unresolved. We introduce TRACE, a method to identify archaic ancestry using features of ancestral recombination graphs...

Fast phenotype simulation for genotype representation graphs.

Aditya Syam, Chris Adonizio, Xinzhu Wei

The Genotype Representation Graph (GRG) is a graph representation of whole genome polymorphisms, designed to encode the variant hard-call information in phased whole genomes. It encodes the genotypes as an extremely compact graph that can be traversed efficiently, enabling dynamic programming-style algorithms on applications such as...