University of the Basque Country researchers decode transcriptome for grey mullet

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.