Genomics
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Independent evolutionary trajectories of genomic repeats and non-repeat genome features in Actinomycetota
Genomic repeats, particularly simple sequence repeats, influence genome stability and gene regulation. While many genomic traits exhibit phylogenetic signal and pulsed evolution, repeat elements have rarely been examined in a comparative framework, and their evolutionary relationships with other genome features remain poorly understood. We contrasted the trait evolution of genomic repeats with non-repeat traits across diverse actinobacterial orders, testing for phylogenetic signal,...
Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes
Cancer genome analysis relies on standard human reference genomes but detecting somatic alterations in highly repetitive or individual-specific regions remains challenging. We developed the Personalized Reference genome-based Cancer Genome Analysis Pipeline (PRCGAP), to our knowledge, the first comprehensive pipeline integrating haplotype-resolved analyses of somatic point mutations, structural variants, copy number, and DNA methylation on personalized diploid reference genomes. We applied...
Comparative genomics reveals extensive genomic conservation and limited microdiversification among Xenorhabdus bovienii isolates recovered from a single Steinernema feltiae isolation event.
Xenorhabdus bovienii is a symbiotic bacterium associated with entomopathogenic nematodes of the genus Steinernema. Comparative genomic analyses of closely related isolates provide an opportunity to investigate fine-scale diversification, genome plasticity, and the evolutionary processes shaping symbiotic bacterial populations. Here, we analyzed four X. bovienii isolates (XenUTI4.1-XenUTI4.4) recovered from a single Steinernema feltiae isolation event using comparative genomics approaches...
ERGA-BGE reference genomes of Hyalomma lusitanicum and its obligate Francisella endosymbiont as a genomic resource for One Health research
Hyalomma lusitanicum is a characteristic tick species of the western Mediterranean region, with a well-established distribution across the Iberian Peninsula. It is strongly associated with wild ungulates, particularly red deer, as well as livestock, to which it can transmit a wide range of pathogens, including viruses, bacteria, and protozoa. Here, we present three genomic resources for H. lusitanicum: a scaffold-scale nuclear genome, the complete mitochondrial genome, and the complete...
In a first, scientists translated an entire viral genome so a quantum computer could read and analyze it
In a first, scientists translated an entire viral genome so a quantum computer could read and analyze it Scientists have uploaded a viral genome to a quantum computer, marking an important step for the future of quantum-enabled advancements in biology. Scientists say they have uploaded a real genome to a quantum computer for the first time, marking an important step in applying the emerging technology to biology. The researchers encoded the entire genome of the hepatitis D virus (HDV) onto a...
Ultra-Fast Implementation of Multivariate GWAS in Genomic SEM Using Flexible Analytic Estimation
Many medical, physiological, and psychiatric traits and disorders are highly polygenic and exhibit complex patterns of genetic sharing and differentiation. In 2018, we introduced Genomic Structural Equation Modelling (Genomic SEM) as a formal framework and free, open source, R-based software for modelling the multivariate genetic architecture of both continuous and binary Genome-Wide Association Study (GWAS) phenotypes, interrogating their joint and distinct functional genomic pathways, and...
Overlooked DNA structures help organize the genome
Overlooked DNA structures help organize the genome Lisa Lock Scientific Editor Robert Egan Associate Editor Northwestern Medicine scientists have discovered that little-studied DNA structures play a central role in organizing the human genome and controlling gene activity, according to a new study published in the Proceedings of the National Academy of Sciences. The study revealed that G-quadruplexes (G4s)—four-stranded DNA structures—directly interact with a key genome-organizing protein...
First whole-genome sequence of a Greenland shark holds clues to their extreme longevity
First whole-genome sequence of a Greenland shark holds clues to their extreme longevity A genomic study of Greenland sharks, thought to be the longest-lived vertebrates on the planet, is hinting at the secrets to their epic lifespan and cancer resistance. The first-ever whole-genome sequence of a Greenland shark has revealed genetic clues to how the animals avoid cancer and live for hundreds of years. The work may pave the way to a better understanding of age-related diseases in humans.
TgmRHel drives unified RNA processing of coxI mRNA generated from a complex mitochondrial genomic context
The mitochondrial genome of Toxoplasma gondii is highly fragmented and recombination-prone, creating a structurally dynamic genetic landscape. How such a genome is used efficiently to produce functional mRNAs remains unclear: it is unknown whether transcription draws from many alternative genomic configurations or a restricted subset, and how any resulting precursor RNAs are processed into mature transcripts. More broadly, mitochondrial RNA processing mechanisms in this system are poorly...
Optical genome mapping identifies source-associated structural variant differences across early-passage human iPSCs
Background: Induced pluripotent stem cells (iPSCs) are an important model for studying human diseases in vitro. However, previous studies have shown that iPSC reprogramming and extended cell culture can introduce genomic structural variants (SVs). Technologies like karyotyping, CNV microarrays, and whole-genome sequencing have limitations in resolution, sensitivity, or the ability to detect large and complex structural variants compared to optical genome mapping (OGM).