Parasite Genomics, 1st ed. 2021
Methods and Protocols
Methods in Molecular Biology Series, Vol. 2369

Part I: Novel Sequencing and Bioinformatic Pipelines for the Study of Parasite Genomes

1. Nanopore Long Read DNA Sequencing of Protozoan Parasites: Hybrid Genome Assembly of Trypanosoma cruzi

            Florencia Díaz-Viraqué, Gonzalo Greif, Luisa Berná, and Carlos Robello

2. Chromosomes Conformation Capture Coupled with Next Generation Sequencing (Hi-C) in Plasmodium falciparum

            Mohit Gupta, Todd Lenz, and Karine G. Le Roch

3. Sequencing and Reconstructing Helminth Mitochondrial Fenomes Directly from Genomic Next-Generation Sequencing Data

            Nikola Palevich and Paul Haydon Maclean

4. Automated Phylogenetic Analysis Using Best Reciprocal BLAST

            Erin R. Butterfield, James C. Abbott, and Mark C. Field

Part II: Diagnostic Approaches Using Genomic Tools

5. An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example

            Jenny G. Maloney, Nadja S. George, Aleksey Molokin, and Monica Santin

6. Giardia duodenalis: Detection by Quantitative Real-Time PCR and Molecular Diversity

            Alejandro Dashti, Pamela C. Köster, and David Carmena

Part III: Host-Parasite Interactions: Deciphering Gene Function and Molecular Processes in Parasites

7. Conditional Gene Deletion in Mammalian and Mosquito Stages of Plasmodium berghei Using Dimerizable Cre Recombinase

            Priyanka Fernandes, Manon Loubens, Olivier Silvie, and Sylvie Briquet

8. Coupling Auxin-Inducible Degron System with Ultrastructure Expansion Microscopy to Accelerate the Discovery of Gene Function in Toxoplasma gondii

9. Genome-Wide Analysis of RNA-Protein Interactions in Plasmodium falciparum Using eCLIP-Seq

            Thomas Hollin, Steven Abel, and Karine G. Le Roch

10. Transcriptional Analysis of Tightly Synchronized Plasmodium falciparum Intraerythrocytic Stages by RT-qPCR

            Núria Casas-Vila, Anastasia K. Pickford, Harvie P. Portugaliza, Elisabet Tintó-Font, and Alfred Cortés

11. Analysis of the Interaction between Plasmodium falciparum-Infected Erythrocytes and Human Endothelial Cells Using a Laminar Flow System, Bioinformatic Tracking and Transcriptome Analysis

            Yifan Wu, Philip Bouws, Stephan Lorenzen, Iris Bruchhaus, and Nahla Galal Metwally

12. Integration of Genomic and Transcriptomic Data to Elucidate Molecular Processes in Babesia divergens

            Luis Miguel González, Elena Sevilla, Miguel Fernández-García, Alejandro Sánchez-Flores, and Estrella Montero

13. Integration of Functional Genomic, Transcriptomic, and Metabolomic Data to Identify Key Features in Genomic Expression, Metabolites, and Metabolic Pathways of Babesia divergens

            Miguel Fernández-García, Alejandro Sanchez-Flores, Luis Miguel González, Coral Barbas, Mª Fernanda Rey-Stolle, Elena Sevilla, Antonia García, and Estrella Montero

14. Genome Analysis of Programmed DNA Elimination in Parasitic Nematodes

            Jianbin Wang

15. Helminth Microbiota Profiling Using Bacterial 16S rRNA Gene Amplicon Sequencing: From Sampling to Sequence Data Mining

            Fabio Formenti, Gabriel Rinaldi, Cinzia Cantacessi, and Alba Cortés

Part IV: Genomics of Parasite-Derived Extracellular Vesicles

16. Methods for the Isolation and Study of Exovesicle DNA from Trypanosomatid Parasites

            Lina María Orrego, Romina Romero, Antonio Osuna, and Luis M. de Pablos

17. Isolation and Analysis of MicroRNAs from Extracellular Vesicles of the Parasitic Model Nematodes Nippostrongylus brasiliensis and Trichuris muris

            Ramon M. Eichenberger

Includes cutting-edge techniques

Provides step-by-step detail essential for reproducible results

Contains key implementation advice from the experts