Laura Núñez-Pons

Laura Núñez-Pons

May 15, 2015

Group 6 Copy 1,004
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Sequencing: DNA Next Generation Sequencing

Most of the requested funding for our project is to be used in DNA Next generation Sequencing: an approach that will reveal us with the information to resolve the identity of the microbes in our corals. We thought that at this point, maybe for some of you the concept and the way DNA sequencing works could be a bit obscure, and thus we decided to make a brief explanatory walk on this amazing and revolutionary modern technique.

DNA stands for DeoxyriboNucleic Acid. It is the molecule that encodes the genetic information to allow the development and functioning of all known living beings. In the DNA, information is encoded by 4 canonical characters called nucleotides:Thymine (T), Adenine (A), Cytosine (C), and Guanine (G). These combine in linear manner, and sequencing is the tool for scientists to determine the physical order of these codifying bases or nucleotides within a molecule of DNA. Most DNA in nature consist of two strands of nucleotides coiled around each other to form a double helix, which then form the so-called chromosomes.

Decodifying DNA sequences has become indispensable for biological research, and in applied fields such as medical diagnosis, biotechnology, forensics, virology etc… The first DNA sequences were obtained in the early 1970s by using laborious and highly expensive methods unreachable by many researching laboratories.

DNA sequencing has become easier and orders of magnitude faster and cheaper thanks to Next Generation Sequencing platforms developed in the mid to late 1990s and implemented commercially in the 2000. The rapid speed of DNA sequencing today, and the great quantity of data obtained with modern technology has been key to accomodate this tool for all the relevant disciplines mentioned previously.

In parallel, the large quantities of data produced by DNA NGS sequencing have also required development of new challenging computer programs and pipelines for sequence analysis. Indeed, the new generation of molecular biologists require now a well-build computational training in order to manage and interpret their results.

But, returning to us: how does NGS (New Generation Sequencing) will allow us to identify the microbes present in our corals?. This will be achieved by what is called 'DNA barcoding'. This concept is based on the fact that some portions in an organism's DNA have been observed to provide a "barcode" that characterizes the different species in nature, and allows to differ them one another. The method hence uses such short genetic marker regions to identify organims as belonging to particular species.

In our case there are two marker regions that will be used to characterize our coral microbiomes. The so-called 'ITS-2' marker permits to identify all the diversity of Symbiodinium associated microalgae; whereas the '16S' region, will provide us the barcodes to resolve which bacteria and archaea are present in our coral colonies.

We hope now you have a better picture of what we are about to proceed to do, now that we happily got our requested funding. Once the DNA has been extracted from our coral sub-samples, which will happen within the next 2 weeks, we will submit this genetic material extracted from all the colonies of the study, including bleached, recovered and resistant corals, to Next Generation Sequencing under MISeq approach (Illumina Platform). Afterwards, intense bioinformatic analyses on our labtops and on 'supercomputers' in our Lab will be run for hours, which will reveal the dynamics in the microbial compartment of our samples during the bleaching and the recovery events. We will keep you well posted!...


Mahalo!...

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  • Richard Honour
    Richard HonourBacker
    Laura: Great explanation. My sequencing work will be a bit different than yours, primarily because our targets will be sequences that code for enzymes in a synthesis pathway, and in our forest/sewage sludge fungi, that will mean in microbes that have real chromosomes, i.e., fungi. I wish you were doing my project. Richard
    May 15, 2015

About This Project

Last summer, coral reefs in Hawaii turned white when high ocean temperatures caused corals to lose the microbes that normally give them color. These microbes also provide nutrition and disease-protection to corals, and without them, "bleached" corals often die. However, corals can survive—and even adapt—if their healthy microbes come back. Now, we are tracking coral recovery in Hawaii up close to understand how the fate of these corals, and even the future of coral reefs, may depend on microbes.

Blast off!

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