Marine Genomics: Methods and Protocols

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-Coln 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 Nez-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