This detailed volume provides an overview of recent advances in the application of genomic technologies in several domains of marine biology, raising awareness of various DNA- and RNA-based technologies. Genomic methods are essential in identifying previously undetected taxonomic (e.g. DNA barcoding), genetic (e.g. sequencing), and functional (e.g. gene expression, analysis of metabolites) diversity, as shown in the chapters of this book, with sections focusing on next generation sequencing (NGS) technologies, bioinformatics in marine genomics research, marine biotechnology, as well as a variety of methods successfully applied in fish. Written for the highly successful
series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical,
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Table of Contents
1. Mitochondrial Genome of Non-Model Marine Metazoans by Next-Generation Sequencing (NGS)
Tullia I. Terraneo, Kiruthiga G. Mariappan, Zac Forsman, and Roberto Arrigoni
2. Genome-Wide DNA Methylation Protocol for Epigenetics Studies
Annalaura Mancia
3. Transcriptome Mining to Identify Genes of Interest: From Local Databases to Phylogenetic Inference
Daniele De Luca and Chiara Lauritano
4. Detecting Structural Variants and Associated Gene Presence-Absence Variation Phenomena in the Genomes of Marine Organisms
Marco Sollitto, Nathan J. Kenny, Samuele Greco, Carmen Federica Tucci, Andrew D. Calcino, and Marco Gerdol
5. From Sequences to Enzymes: Comparative Genomics to Study Evolutionary Conserved Protein Functions in Marine Microbes
Angelina Cordone, Alessandro Coppola, Angelica Severino, Monica Correggia, Matteo Selci, Antonio Cascone, Costantino Vetriani, and Donato Giovannelli
6. VenomFlow: An Automated Bioinformatic Pipeline for Identification of Disulfide-Rich Peptides from Venom Arsenals
Eleonora Achrak, Jennifer Ferd, Jessica Schulman, Trami Dang, Konstantinos Krampis, and Mande Holford
7. Population Genomics Analysis with RAD, Reprised: Stacks 2
Angel G. Rivera-Colón and Julian Catchen
8. A Metabarcoding Protocol to Analyze Coastal Planktic Communities Collected by Desalination Plant Filters: From Sampling to Bioinformatic Exploratory Analyses
Matteo Cecchetto, Andrea Di Cesare, Ester Eckert, Isabella Moro, Diego Fontaneto, and Stefano Schiaparelli
9. Barcoding of Antarctic Marine Invertebrates: From Field Sampling to Lab Procedures
Stefano Schiaparelli, Maria Chiara Alvaro, Matteo Cecchetto, and Alice Guzzi
10. DNA Barcoding Procedures for Taxonomical and Phylogenetic Studies in Marine Animals: Porifera as Case Study
Laura Núñez-Pons, Valerio Mazzella, Francesca Rispo, Jana Efremova, and Barbara Calcinai
11. Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction
Dominique A. Cowart, Katherine R. Murphy, and C.-H. Christina Cheng
12. Metataxonomic Analysis of Bacterial Diversity Associated with Marine Organisms
Nadia Ruocco, Roberta Esposito, Valerio Zupo, and Maria Costantini
13. From Sequences to Enzymes: Heterologous Expression of Genes from Marine Microbes
Angelica Severino, Alessandro Coppola, Monica Correggia, Costantino Vetriani, Donato Giovannelli, and Angelina Cordone
14. Expression of Recombinant Cold-Adapted (Hemo)Globins from Marine Bacteria
Daniela Giordano and Cinzia Verde
15. Isolation of UV-Resistant Marine Bacteria by UV-C Assays
Daniela Coppola, Cinzia Verde, and Daniela Giordano
16. Fractionation Protocol of Marine Metabolites
Genoveffa Nuzzo, Emiliano Manzo, Carmela Gallo, Giuliana d'Ippolito, and Angelo Fontana
17. Detection and Quantification of Small Non-Coding RNAs in Marine Diatoms
Alessandra Rogato and Angela Falciatore
18. Optimized Proteolistic Protocol for the Delivery of the Cas9 Protein in Phaeodactylum tricornutum
Monia Teresa Russo, Anna Santin, Alessandra Rogato, and Maria Immacolata Ferrante
19. Production of a Chimeric Mouse-Fish Monoclonal Antibody by the CRISPR/Cas9 Technology
Alessia Ametrano and Maria Rosaria Coscia
20. Identification, Characterization, and Expression Analysis of Immunoglobulin Genes from Antarctic Fish by PCR Methods
Alessia Ametrano and Maria Rosaria Coscia
21. Physical Mapping of Repeated Sequences on Fish Chromosomes by Fluorescence In Situ Hybridization (FISH)
Laura Ghigliotti, Juliette Auvinet, and Eva Pisano
22. Functional Genomics of Fish Erythrocytes
Mikko Nikinmaa and Amélie Crespel
23. Stain-Free Approach for Western Blot Analysis of Zebrafish Embryos
Jianmin Xue and Paola Corti
24. Proteomics of Fish White Muscle and Western Blotting to Detect Putative Allergens
Liliana Anjos, Arsenios-Zafeirios Loukissas, and Deborah Mary Power
25. In Vitro Assays for the Bifunctional Acylpeptide Hydrolase (APEH) Enzyme from Antarctic Fish
Carmela Fusco, Bruna Agrillo, Marta Gogliettino, Gianna Palmieri, and Ennio Cocca
