Classification and taxonomy articles from across Nature Portfolio

Metagenomic taxonomic profiling usually relies either on reads or assembled contigs/MAGs. Here, authors present RAT, a tool that integrates taxonomic signals from reads, contigs, and MAGs into one profile with high precision and sensitivity. RAT provides a comprehensive view of the microbiome.

This study introduces SANGO, a method for accurate single-cell annotation leveraging genomic sequences around accessibility peaks within single-cell ATAC sequencing data. SANGO consistently outperforms existing methods across diverse datasets for identification of cell type and detection of unknown tumor cells. SANGO enables the discovery of cell-type-specific functional insights through expression enrichment, cis-regulatory chromatin interactions and motif enrichment analyses.

Analysis of the virus community associated with red algal mats in Yellowstone National Park shows it to be dominated by Megaviricetes, with resident virus lineages being of ancient origin and encoding genomic footprints of adaptation to thermophily.

Inspired by active learning approaches, we have developed a computational method that selects minimal gene sets capable of reliably identifying cell-types and transcriptional states in large sets of single-cell RNA-sequencing data. As the procedure focuses computational resources on poorly classified cells, active support vector machine (ActiveSVM) scales to data sets with over one million cells.

This month’s Genome Watch highlights the systematic discovery of defence systems, paving the way to decode novel genetic functions and further our understanding of microbial warfare.

A suite of new enzymes reveals more on how Nature breaks down plant-based polysaccharides and how these enzymes might be harnessed in the utilization of plant-based biomass.

Improvements to the Genome Taxonomy Database provide a complete bacterial and archaeal taxonomy.

Researchers identify a broad phylogenetic diversity of nucleocytoplasmic large DNA viruses by mining global-scale metagenomics datasets.

Complementary genomic frameworks for taxonomic classification of viruses infecting bacteria and archaea reveal evolutionary drivers, mosaicism and perspective on the genetic diversity of the tiniest, most abundant biological entities on Earth.