University of the Basque Country researchers decode transcriptome for gray mullet

January 29, 2010

The Cell Biology in Environmental Toxicology research team at the Department of Zoology and Animal Cell Biology at the University of the Basque Country (UPV/EHU) has decoded the transcriptome for the grey mullet. The director of the research project was Mr Ibon Cancio.

On more than one occasion we will have heard that the genome is the library where all the information of each organism is stored. This information is organised in various genes, where the information to synthesise the proteins that carry out most cell functions is stored. The genome also has another type of genetic material that is not in the genes. This is the transcriptome - the part of the genome that is transcribed or is read. In most pluricellular beings it is usually more or less 1.5% of the genome.

This UPV/EHU research team has just decoded the transcriptome of the grey mullet. For a number of years now the researchers have been measuring the quality of river and sea water. For this it was necessary to have an animal capable of living in contaminated areas, one of which is the grey mullet. The aim was to measure the response that this animal has to contamination, in order to better know the quality of surrounding water. Besides, the grey mullet is very abundant in the rivers and sea of the Basque Country. Thus, according to Mr Cancio, it is the appropriate animal model, being very abundant and capable of surviving in contaminated areas.

More than half of the genes

The research was initiated in the Basque fishing port of Ondarroa, gathering a number of grey mullets: males, females, young fish, etc. Organs such as the liver, gills, gonads and brain were extirpated from each and the messenger RNA extracted. These samples of messenger RNA were suitably mixed to ensure that most of the transcriptome of the species would be found in the overall sample. Subsequently, the messenger RNA was converted to complementary DNA.

The samples of complementary DNA were sent to the sequencing department at the University of Newcastle in Britain. This university has a new sequencing system whereby, with just one analysis lasting seven and a half hours, 400,000 cDNA, can be sequenced, each with a length of 250 nucleotides. This was how the UPV/EHU research team obtained all the information about the transcriptome of the grey mullet; 126 million nucleotides, in concrete.

The most laborious task came later - making sense of all the information obtained, i.e. identifying the genes for each sequence, given that the function of the sequence can be found out from the gene. To this end, help from the General Research Services (SGIker) of the UPV/EHU was required.

Following this procedure, 18,332 genes were obtained. The aim was not to identify all the genes of the grey mullet, but more than half of them. With all this information a DNA microchip was developed in order to investigate the response of the mentioned genes to contamination.

For the upcoming year the challenge for the UPV/EHU research team to decode the transcriptome of the slug in order to generate a health profile of the soil.
-end-


Elhuyar Fundazioa

Related Genome Articles from Brightsurf:

Genome evolution goes digital
Dr. Alan Herbert from InsideOutBio describes ground-breaking research in a paper published online by Royal Society Open Science.

Breakthrough in genome visualization
Kadir Dede and Dr. Enno Ohlebusch at Ulm University in Germany have devised a method for constructing pan-genome subgraphs at different granularities without having to wait hours and days on end for the software to process the entire genome.

Sturgeon genome sequenced
Sturgeons lived on earth already 300 million years ago and yet their external appearance seems to have undergone very little change.

A sea monster's genome
The giant squid is an elusive giant, but its secrets are about to be revealed.

Deciphering the walnut genome
New research could provide a major boost to the state's growing $1.6 billion walnut industry by making it easier to breed walnut trees better equipped to combat the soil-borne pathogens that now plague many of California's 4,800 growers.

Illuminating the genome
Development of a new molecular visualisation method, RNA-guided endonuclease -- in situ labelling (RGEN-ISL) for the CRISPR/Cas9-mediated labelling of genomic sequences in nuclei and chromosomes.

A genome under influence
References form the basis of our comprehension of the world: they enable us to measure the height of our children or the efficiency of a drug.

How a virus destabilizes the genome
New insights into how Kaposi's sarcoma-associated herpesvirus (KSHV) induces genome instability and promotes cell proliferation could lead to the development of novel antiviral therapies for KSHV-associated cancers, according to a study published Sept.

Better genome editing
Reich Group researchers develop a more efficient and precise method of in-cell genome editing.

Unlocking the genome
A team led by Prof. Stein Aerts (VIB-KU Leuven) uncovers how access to relevant DNA regions is orchestrated in epithelial cells.

Read More: Genome News and Genome Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.