Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Contains fulltext : 136229.pdf (publisher's version ) (Open Access)BACKGROUND: Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat. RESULTS: Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages. CONCLUSIONS: Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis

Stemcel biology/Regenerative medicine (incl. bloodtransfusion

The landscape of C. elegans 3'UTRs

Three-prime untranslated regions (3'UTRs) of metazoan mRNAs contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3'RACE, full-length cDNAs, and RNA-seq, we define ~26,000 distinct 3'UTRs in Caenorhabditis elegans for ~85% of the 18,328 experimentally supported protein coding genes and revise ~40% of gene models. Alternative 3'UTR isoforms are frequent, often differentially expressed during development. Average 3'UTR length decreases with animal age. Surprisingly, no polyadenylation signal (PAS) is detected for 13% of polyA sites, predominantly among shorter alternative isoforms. Trans-spliced (vs. non-trans-spliced) mRNAs possess longer 3'UTRs and frequently contain no PAS or variant PAS. We identify conserved 3'UTR motifs, isoform-specific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3'UTRs genome-wide and throughout development

Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

NoAlthough the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections