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Whole-genome sequencing (WGS) is used to determine the genetic composition of an organism. This fast-moving field is continually evolving through technical advancements and the development of new bioinformatic tools for analyzing genomic data; however, the basic principles and processes for defining and processing high-quality genome sequence information remain unchanged. Here, we introduce some considerations and describe some commonly used bioinformatic steps for processing raw genome sequence data to generate genome assemblies through to understanding basic population genomics.
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http://dx.doi.org/10.1007/978-1-0716-0467-0_7 | DOI Listing |
Mitochondrial DNA A DNA Mapp Seq Anal
September 2025
Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
Hibernation is an elaborate response strategy employed by numerous mammals to survive in cold conditions that involves active suppression of metabolism. Despite the role of mitochondria as energy metabolism centers during hibernation, the adaptive and evolutionary mechanisms of mitochondrial genes in hibernating animals, like hedgehogs in eulipotyphlan species, are not yet fully understood. In this study, we sequenced and assembled mitochondrial genomes of the hibernating four-toed hedgehog () and the non-hibernating Asian house shrew ().
View Article and Find Full Text PDFPlant Genome
September 2025
Department of Agronomy, Iowa State University, Ames, Iowa, USA.
Crop growth rate is a critical physiological trait for forage and bioenergy crops like sorghum [Sorghum bicolor (L.) Moench], influencing overall crop productivity, particularly in photoperiod-sensitive (PS) types. Crop growth rate studies focus on either a physiological approach utilizing a few genotypes to analyze biomass accumulation or a genetic approach characterizing easily scorable proxy traits in larger populations.
View Article and Find Full Text PDFHypertension
September 2025
Department of Obstetrics and Gynecology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu (Z.W.).
Background: Early-onset preeclampsia poses significant risks to maternal and fetal health, necessitating a deeper understanding of its molecular mechanisms and effective therapeutic strategies.
Methods: Utilizing data from genome-wide association study and Mendelian randomization analysis, we investigated the relationship between mitochondrial DNA copy number and preeclampsia. Transcriptome sequencing, in vitro experiments, and animal studies were conducted to explore the roles of SENP3 and SETD7 in preeclampsia pathogenesis.
Circ Genom Precis Med
September 2025
Feinberg School of Medicine, Northwestern University, Chicago, IL (Z.C., P.G., A.G., G.W.).
Background: Genetic variation contributes to atrial fibrillation (AF), but its impact may vary with age. The Research Program contains whole-genome sequencing of data from 100 574 adult participants with linked electronic health records.
Methods: We assessed clinical, monogenic, and polygenic associations with AF in a cross-sectional analysis, stratified by age: <45 years (n=22 290), 45 to 60 years (n=26 805), and >60 years (n=51 659).
Mult Scler
September 2025
Department of Neurology with Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany.
Description of a patient with multiple sclerosis (MS) who underwent immunotherapy with ocrelizumab and suffered a severe course of tick-borne encephalitis (TBE): A 33-year-old man presented with acute cerebellitis with tonsillar herniation. The initial suspected diagnosis of TBE was confirmed after a significant diagnostic delay, likely caused by negative serological testing due to B-cell depletion from ocrelizumab treatment for underlying MS. TBE diagnosis was made using polymerase chain reaction (PCR) and oligo-hybrid capture metagenomic next-generation sequencing (mNGS) of cerebral spinal fluid and brain biopsy samples which yielded a near-full length TBE Virus (TBEV) genome.
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