Marine Genomics: Methods and Protocols (Methods in Molecular by Sarah J. Bourlat

By Sarah J. Bourlat

This quantity offers the most recent protocols for either laboratory and bioinformatics dependent analyses within the box of marine genomics. The chapters provided within the publication hide quite a lot of themes, together with the sampling and genomics of bacterial groups, DNA extraction in marine organisms, high-throughput sequencing of entire mitochondrial genomes, phylogenomics, SNP discovery, SNP-arrays for species id, electronic PCR-based quantification equipment, surroundings DNA for invasive species surveillance and tracking, microarrays for the detection of waterborne pathogens, DNA barcoding of marine biodiversity, metabarcoding protocols for marine eukaryotes, analytical protocols for the visualization of eukaryotic range, and functions for genomic information to benthic indices for environmental tracking. Written within the hugely successful Methods in Molecular Biology sequence layout, chapters comprise creation to their respective issues, lists of the required fabrics and reagents, step by step, effectively reproducible laboratory protocols, and tips about troubleshooting and keeping off identified pitfalls.

Cutting-edge and thorough, Marine Genomics: equipment and Protocols is a invaluable source for researchers, scholars, and coverage makers within the box of marine biology.

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Remove the top plates (tergum and scutum) using a pair of tweezers (Fig. 9a, b and see Note 22). Grab the animal and pull it out of the shell. Mostly, this results in the soma (body) and cirri appearing without the mantle (see Note 23). 2. A. 5 mL microcentrifuge tube. Homogenize with the plastic pestle in roughly five strokes (see Note 24). Fig. 9 Removing the body of an acorn barnacle from its shell. (a) Grab one of the top opercular plates by inserting tweezers gently through the aperture. Pull gently to remove the plate and to expose the animal.

Check the pellets every 5–10 min. When dry, the DNA pellets look transparent; there should not be any ethanol drops left within the tube and no residual ethanol smell either. 14. In I. balthica, high-quality DNA can be extracted from the head and the abdominal muscle. Any pieces of the gut and its content should be avoided because it would yield highly degraded DNA. In addition, gut contents will lead to contaminant sequences. Before collecting tissue samples, cut the carapace along the dorsal side (being careful not to disturb the gut), remove the gut, and wash the animal in ethanol.

The mantle and potentially fertilized eggs (in the ovary) stay in the shell cavity when the body is pulled out and are discarded (they are not used for the DNA extraction) 38 Marina Panova et al. 3. 5 μL of RNase A. Vortex for 15 s at full speed. Homogenize again with the plastic pestle (2–3 strokes). 4. Incubate the samples for 10 min at 65 °C. Vortex briefly 2–3 times during the incubation. 5. Centrifuge for 3 min at maximum speed. 6. Transfer the supernatant with a pipette into a new microcentrifuge tube.

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