Phylogenomics: Foundations, Methods, and Pathogen Analysis

ISBN-13: 9780323998864 / Angielski

Igor Mokrousov; Egor Shitikov

Opis

Phylogenomics: Foundations, Methods, and Pathogen Analysis offers a deep overview of phylogenomics as a field, compelling recent developments, and detailed methods and approaches for conducting new research. Early chapters introduce phylogenomic taxonomies of organisms and pathogens, phylogenomic networks, phylogenomics of virus virulence, and ancient DNA analysis, with a second section offering methods, detailed descriptions and step-by-step instruction in genome assembly and annotation, horizontal gene transfer studies, Bayesian evaluation, phylogenetic tree building, microbial evolution modeling, and molecular epidemiology. The book's final section offers various examples of phylogenomic analysis across medically significant bacteria and viruses, including Yersinia pestis, Salmonella, Shigella, Vibrio cholera, and Mycobacterium tuberculosis, amongst others.

Spis treści

PART I. GENERAL TOPICS AND FOUNDATIONS 1. Phylogenomic analysis and the origin and early evolution of viruses 2. Genome-based taxonomy of Bacteria 3. Horizontal Gene Transfer and the History of Life 4. Genomic insight into deciphering bacterial outbreaks 5. Evolution of bacterial resistance 6. Evolution of bacterial virulence PART II. METHODS IN THE PHYLOGENOMICS 7. Bayesian Evaluation of Temporal Signal 8. Microbial evolutionary reconstruction in the presence of mosaic sequences 9. Tools for SNP calling and the way to deal with big datasets PART III. PHYLOGENOMICS OF SPECIFIC PATHOGENS 10. Yersinia pestis 11. Salmonella 12. Shigella 13. Phylogenomic diversity within Corynebacterium diphtheriae, a re-emerging threat to global public health 14. Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis 15. Mycobacterium kansasii 16. Leptospira 17. Measles virus 18. Human immunodeficiency virus 19. Respiratory RSV viruses 20. Flaviviruses 21. Staphylococcus aureus 22. Genomic research of ancient pathogens in Central Asia 23. Cryptococcus neoformans/gattii 24. Mycobacterium leprae phylogenomics