UdeC researchers have next-generation genomic sequencing

Sunday, 24 th November 2013

Knowing details of the DNA sequences is essential for scientific advancement. This process has been strongly developed in recent times, which has significantly accelerated research and discoveries in various scientific fields. Current techniques, that allows to do this high speed sequencing, has been of great importance for large-scale projects, starting with the Human Genome Project, which took a period close to the 10 years and a great investment- initiatives that allow to decipher the genetic information of various species in a time much smaller.

Aware of the importance, researchers at the Interdisciplinary Center for Aquaculture Research (Interdisciplinary Center for Aquaculture Research, INCAR) from Universidad de Concepción, recently acquired a massive sequencer, high-tech equipment and the first for genomic sequencing that is installed in Southern Chile, and the third in the country. The massive sequencer now works in the laboratory of Aquatic Biotechnology and Genomics Biotechnology Center UdeC.

Cristian Gallardo, INCAR deputy, explained that this computer "if it is true is designed for aquaculture issues, it also aims to enable UdeC researchers, from other specialties, can generate genomic projects in the areas of biomedicine, pharmacy or natural resources, leading genomics research transcendence ".

Massive sequencing equipment, Illumina Miseq brand, has the ability to generate an amount equivalent to five human genomes information and required an investment of 100 million pesos, to which accessory equipment by others is added 150 million pesos. "On the other hand, they have formed inside UdeC specialists in handling this equipment, which is very sophisticated ", said Dr. Gallardo.

The DNA of sea lice

The massive sequencer is already in operation and, under the INCAR, researchers will launch the first publication with Caligus rogercresseyi sequencing (commonly known as sea lice), a parasite that attacks the salmon and generates, annually, losses close to 480 million dollars per year. Dr. Gallardo, who is also principal investigator on the line Genomics in Aquaculture Technology INCAR, he explained that this paper is an important contribution to the international scientific community with the first description of this parasite transcriptome.

"This research will improve the treatment of this pest. One of the things that are currently done in salmon farming is to apply insecticide on these sea lice. This entails not only environmental problems, but a large economic cost, which makes it very unsustainable. On the other hand, with time, these parasites create resistance to insecticides that are applied to them, making them unusable. With the genetic information that we have deciphered, it would be possible to see the part of the genome that would be, for example, involved in such resistance. Also you can see if there are differences in the populations of these lice affecting farms, to discover how different they are, on a genetical level, between them. It is a strong theme of sustainability that will attack our center through this latest technology ", he said.

Among other research that will be developed under the wing of this new equipment it is obtaining the conger's genome - emblematic species of Chile, which is being cultivated commercially, to understand relative aspects of their disease, reproduction, as a way to improve their cultivation process.

"The massive sequencing equipment will allow, as well, to work with major salmon diseases, so to understand their defense mechanisms and how infection of these pathogens occurs. That is also an important topic of sustainability, because if you understand how pathogens attack, you can avoid indiscriminate use of antibiotics - which is one of the great criticisms made to the chilean salmon culture -, and better vaccines or therapeutic methods can be tested and improved to prevent the spread of disease, mainly ISA virus and bacterial pathogen causing the SRS disease", Dr. Gallardo.
Finally, the researcher points out that this equipment will also be used in nutritional aspects. “For example, one of the problems of sustainability in aquaculture is that salmon are fed with animal protein. This implies to liquidate all stocks of fish in the sea to transform them into the pellets that salmon eat, which is a very complex sustainability topic. It was always meant to give them vegetable proteins; however, salmon do not accept them because they are not developmentally ready for such proteins. This will let us understand the mechanisms, at a fish digestive physiology level, that prevent that to happen. For this, postdoctoral researchers have joined the INCAR to be devoted to the subject", said Dr. Gallardo.

In this regard he concluded by saying that, apart from bringing the technology, very valuable human resources have come from Spain, Portugal and Japan.

Source: Panorama UdeC, Dirección de Relaciones Institucionales, Unidad de Asuntos Públicos., 24 th November 2013.