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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
Integration of 168,000 samples reveals global patterns of the human gut microbiome
We use this compendium to evaluate geographic and technical effects on microbiome variation. We find that regions such as Central and Southern Asia differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America and that composition alone can be used to predict a sample’s region of origin.
- 168,000 public 16S gut microbiome samples processed and integrated at microbiomap.org
- Microbiome composition and diversity differ widely between world regions
- Technical factors like amplicon choice associate with compositional differences
- Classifiers trained on compendium data can infer world regions from composition
submitted by: Istvan Albert
Brain development is similar in Neanderthals and modern humans
Neanderthal brains were similar in size to those of modern humans but differed in shape. What we cannot tell from fossils is how Neanderthal brains might have differed in function or organization of brain layers such as the neocortex. Pinson et al. have now analyzed the effect of a single amino acid change in the transketolase-like 1 (TKTL1) protein on production of basal radial glia, the workhorses that generate much of the neocortex (see the Perspective by Malgrange and Nguyen). Modern humans differ from apes and Neanderthals by this single amino acid change.
See also: https://x.com/AgBioWorld/status/1575106305152327680
submitted by: Istvan Albert
cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters (academic.oup.com)
Here, we present cblaster, a Python-based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface. It generates outputs that enable intuitive visualizations of large datasets and can be readily incorporated into larger bioinformatic pipelines.
Github: https://github.com/gamcil/cblaster
submitted by: Istvan Albert
Low level contamination confounds population genomic analysis | bioRxiv (www.biorxiv.org)
Using a standard base calling pipeline, we found that contaminated genomes superficially appeared to produce good quality genome data. Yet as little as 5-10% genome contamination was enough to change phylogenetic tree topologies and make contaminated strains appear as hybrids between lineages (genetically admixed). We recommend the use of B-allele frequency plots to screen genome resequencing data for intra-species contamination.
submitted by: Istvan Albert
Complete human recombination maps | Nature (www.nature.com)
Using whole-genome sequence data in families, we estimate the number of NCOs transmitted from parent to offspring and derive complete, sex-specific recombination maps including both NCOs and COs. Mothers have fewer but longer NCOs than fathers, and oocytes accumulate NCOs in a non-regulated fashion with maternal age.
submitted by: Istvan Albert
x.com (x.com)
Complete human recombination maps https://nature.com/articles/s41586-024-08450-5 - continuation of 25 years of work building recombination maps.
submitted by: Istvan Albert
Diversity and consequences of structural variation in the human genome | Nature Reviews Genetics (www.nature.com)
The biomedical community is increasingly invested in capturing all genetic variants across human genomes, interpreting their functional consequences and translating these findings to the clinic. A crucial component of this endeavour is the discovery and characterization of structural variants (SVs), which are ubiquitous in the human population, heterogeneous in their mutational processes, key substrates for evolution and adaptation, and profound drivers of human disease. The recent emergence of new technologies and the remarkable scale of sequence-based population studies have begun to crystalize our understanding of SVs as a mutational class and their widespread influence across phenotypes. In this Review, we summarize recent discoveries and new insights into SVs in the human genome in terms of their mutational patterns, population genetics, functional consequences, and impact on human traits and disease. We conclude by outlining three frontiers to be explored by the field over the next decade.
submitted by: Istvan Albert
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