Files
Abstract
The advent of high throughput sequencing technologies makes it possible to address biological questions at the genome-wide scale. Analysis of these data creates unprecedented opportunities to explore the functions and dynamics of the genomes of large numbers of prokaryotes and non-model eukaryotic species. Herein I combine a new approach for allele-based subtyping and study of the genome of the pathogenic bacteria Listeria monocytogenes, and the analysis of the genome of the North American song sparrow (Melospiza melodia), selected for its behavioral, ecological, and biomedical importance. I developed an open-source software tool (Haplo-ST) to provide whole-genome multi locus sequence typing (wgMLST) of Listeria monocytogenes from Illumina whole-genome sequencing data, while improving standardization and data exchangeability worldwide. Along with allelic profiles, this tool also generates allele sequences and identifies paralogous genes present in each isolate, which is extremely useful for evaluating phylogenetic relationships between closely related strains. More broadly, Haplo-ST is flexible and can be adapted to characterize the genome of any haploid organism simply by installing an organism-specific gene database. This tool was used to characterize and differentiate between two groups of L. monocytogenes isolates obtained from the natural environment and poultry processing plants. This tool was also used to study the patterns of genetic diversity and linkage disequilibrium in a large and diverse collection of L. monocytogenes isolates. We expect that Haplo-ST will serve as a valuable resource for accurately subtyping and evaluating relationships among bacterial isolates for routine surveillance, outbreak investigations and source tracking.
We used genome assembly and annotation of the North American song sparrow (Melospiza melodia) to identify genomic coordinates of protein-coding genes, microsatellites, repeat elements, transposable elements and several categories of non-coding RNA. The protein-coding genes were assigned with functional annotations and the genome assembly of the song sparrow was compared to that of several closely related birds. The genomic resources developed during this study will serve as valuable resources for facilitating studies contributing to biomedical research and in population genomic and comparative genomic studies of closely related species.