Phylogenomics

Foundations, Methods, and Pathogen Analysis

1st Edition - May 1, 2024
Editors: Igor Mokrousov, Egor Shitikov
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 8 8 6 - 4
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 1 3 0 9 - 6

Phylogenomics: Foundations, Methods, and Pathogen Analysis offers a deep overview of phylogenomics as a field, compelling recent developments, and detailed methods and approache… Read more

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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 analysis of viruses and bacteria, deciphering bacterial outbreaks, and evolution of drug resistance and virulence, with a second section on methods offering instruction in tools for SNP calling and dealing with big datasets, use of Bayesian approach in molecular epidemiology, bacterial evolution modeling and evolutionary reconstruction in the presence of mosaic sequences. Part 3 offers various examples of phylogenomic analysis across medically significant bacteria and viruses, including Yersinia pestis, Salmonella, Mycobacterium tuberculosis, HIV-1, measles virus as well as ancient pathogens research.

PART I. GENERAL TOPICS AND FOUNDATIONS

1. Phylogenomic analysis and the origin and early evolution of viruses
Gustavo Caetano-Anolles

2. Application of Next Generation Sequencing for Genetic and Phenotypic Studies of Bacteria
Prasit Palittapongarnpim

3. Genomic insight into deciphering bacterial outbreaks
Fernando Gonzalez-Candelas

4. Drug resistance in bacteria, molecular mechanisms and evolution
Urvashi B. Singh

5. Virulence evolution of bacterial species
João Perdigão, Isabel Portugal, Pedro Gomes and Rita Elias

PART II. METHODS IN THE PHYLOGENOMICS

6. Modeling evolutionary changes of k-mer patterns of bacterial genomes
Oleg N. Reva

7. Clock Rates and Bayesian Evaluation of Temporal Signal
Nour Gharbi, Emilie Rousseau, and Thierry Wirth

8. Microbial evolutionary reconstruction in the presence of mosaic sequences
Pakorn Aiewsakun

9. Tools for SNP calling and the way to deal with big datasets
Adrien Le Meur, Rima Zein-Eddine, Ombeline Lamer, Fiona Hak, Gaëtan Senelle, Jean-Philippe Vernadet, Samuel O’Donnell, Ricardo Rodriguez de la Vega, and Guislaine Refregier

PART III. PHYLOGENOMICS OF SPECIFIC PATHOGENS

10. Phylogenomics of Yersinia pestis
Yarong Wu, Xiuwei Qian, Xiujuan Zuo, Yujun Cui, and Ruifu Yang

11. Salmonella Phylogenomics
Chenghao Jia, Haiyang Zhou, Zining Wang Yuhao Liu, and Min Yue

12. The phylogenomics of Shigella spp.
Kate S. Baker, Jane Hawkey, Danielle Ingle, Sydney L Miles, and Hao Chung The

13. Phylogenomic diversity within Corynebacterium diphtheriae, a re-emerging threat to global public health
Vartul Sangal and Andreas Burkovski

14. Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis
Egor Shitikov, Igor Mokrousov, and Dmitry Bespiatykh

15. Mycobacterium kansasii
Tao Luo

16. Taxonomy and phylogenomics of Leptospira
Cecilia Nieves, Samuel G. Huete, Frédéric Veyrier, and Mathieu Picardeau

17. Phylogenomics and evolution of Measles virus
Sunitha Manjari Kasibhatla,, Sunil R. Vaidya, Mohan M. Kale and Urmila Kulkarni-Kale

18. Phylogenomics of HIV-1
Ana Abecasis, Anne-Mieke Vandamme and Marta Pingarilho

19. Respiratory syncytial virus
Mitsuru Sada, Tatsuya Shirai, and Hirokazu Kimura

20. Phylogenomics of Flaviviruses
Qi Li and Ran Wang

21. How clonal is Staphylococcus aureus?
Michel Tibayrenc

22. Genomic research of ancient pathogens in Central Asia
Lyazzat Musralina, Elmira Khussainova, Nazym Altynova, and Leyla Djansugurova

23. Subspecific nomenclature of the Cryptococcus neoformans/gattii complex and the predominant clonal evolution (PCE) model
Michel Tibayrenc

24. Phylogenomics of Mycobacterium leprae
Mukul Sharma, Purna Dwivedi, Jaimin Chodvadiya, Neha Bhardwaj, Afzal Ansari, Gayatri Sondhiya, and Pushpendra Singh

Igor Mokrousov

Igor Mokrousov, 53 years old, PhD, DSc, is the Head of Laboratory of Molecular Epidemiology and Evolutionary Genetics at St. Petersburg Pasteur Institute, Russia. His research interests include study of evolution, phylogenomics, and molecular epidemiology of tuberculosis; phylogeography of Mycobacterium tuberculosis and co-evolution with humans; molecular mechanisms and genotypic detection of drug resistance. His current projects focus on the application of next-generation sequencing for genome-wide analysis to understand the pathogenetic characteristics and evolutionary trajectory of various M. tuberculosis lineages and emerging clones. Dr Mokrousov made a recognized contribution to the study of human-M. tuberculosis coevolution and put forward a hypothesis that evolutionary histories of H. sapiens and human pathogens are comirrored and coshaped. He proposed a new simple measure of genetic distance between geographic populations within a microbial species based on the observed difference in the frequencies of its genotypes.

Affiliations and expertise

Head of the Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, Russia

Egor Shitikov

Egor Shitikov, PhD, is the Head of Laboratory of Molecular Genetics of Microorganisms at Federal Research and Clinical Center of Physical-Chemical Medicine, Russia. His research interests are closely related to the systematic analysis of Mycobacterium tuberculosis: phylogenetic relationship of various strains, their definition and classification; the search for new drug-resistance determinants, virulence factors, and pathogenicity; development of rapid screening systems for certain pathogen groups; experiments on model organisms. The current topic focuses on the deep machine learning methods in Mycobacterium tuberculosis genomics for the building of an open platform for the analysis of the pathogen’s evolutionary signatures.

Affiliations and expertise

Head of the Laboratory of Molecular Genetics of Microorganisms, Federal Research and Clinical Center of Physical-Chemical Medicine, Russia