bioRxiv Subject Collection: Genomics

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Breeding Program Optimization for Genomic Selection in Winter Wheat [NEW RESULTS]

Developing methodologies in the fields of phenomics and genomic prediction have the potential to increase the production of crop species by influencing germplasm improvement. The integration of these technologies into germplasm improvement and breeding programs requires evidence that there will be a direct economic benefit to the program. We determined...

Mapping of DNA damage genome-wide at nucleotide resolution by circle-damage-sequencing [NEW RESULTS]

To establish relationships between mutations, for example in cancer genomes, and possible mechanisms linked to DNA damage, it is necessary to know at what sequence positions of the genome the damage occurs. However, it has been challenging to specifically map DNA damage at the nucleotide level of resolution and genome-wide with high sensitivity. Here,...

Genomics of Human Respiratory Syncytial Virus Vaccine Attenuation [NEW RESULTS]

The human orthopneumovirus (HRSV) is a major cause of lower respiratory tract infection in children worldwide. Despite decades of efforts, no vaccine is available. In this work, we report mutations that are frequent in vaccine candidates and rare in wild-type genomes, taking into account all the publicly available HRSV sequence data. These mutations...

Differential gene expression in brain and liver tissue of Wistar rats after rapid eye movement sleep deprivation [NEW RESULTS]

Sleep is essential for the survival of most living beings. Numerous researchers have identified a series of genes that are thought to regulate sleep-state or the deprived state. As sleep has significant effect on physiology, we believe that lack of sleep or particularly REM sleep for a prolonged period would have a profound impact on various body tissues....

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice [NEW RESULTS]

Genetically modified mouse models of ageing are the living proof that lifespan and healthspan can be lengthened or shortened, yet the molecular mechanisms behind these opposite phenotypes remain largely unknown. In this study, we analysed and compared gene expression data from 10 long-lived and 8 short-lived mouse models of ageing. Transcriptome-wide...

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes [NEW RESULTS]

Comparative analysis of 162 (nearly) complete genomes of Asgard archaea, including 75 not reported previously, substantially expands the phylogenetic and metabolic diversity of the superphylum Asgard, with six additional phyla proposed. Phylogenetic analysis of universally conserved genes does not strongly support the origin of eukaryotes from within...

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes [NEW RESULTS]

Comparative analysis of 162 (nearly) complete genomes of Asgard archaea, including 75 not reported previously, substantially expands the phylogenetic and metabolic diversity of the superphylum Asgard, with six additional phyla proposed. Phylogenetic analysis of universally conserved genes does not strongly support the origin of eukaryotes from within...

Population and species diversity at mouse centromere satellites [NEW RESULTS]

Centromeres are satellite-rich chromatin domains that are essential for chromosome segregation. Centromere satellites evolve rapidly between species but little is known about population-level diversity across these loci. We developed a k-mer based method to quantify centromere copy number and sequence variation from whole genome sequencing data. We...

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim [NEW RESULTS]

Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC), causing tuberculosis (TB) in humans. L1 and L3 are endemic to the Rim of the Indian Ocean, the region that accounts for most of the world's new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Here we analyzed 2,938 L1 and 2,030...

Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen Enterococcus faecium [NEW RESULTS]

Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated as clade A1 and that plasmids are major contributors to the emergence...

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