The Lynxgenomics project has completed the assembly of the first draft of the lynx genome, after two and a half years of hard work using cutting edge technologies. This means achieving a major milestone for the project, although this is not the end of the path, because the structure obtained is now like a mute city map, without street or square names, so it is of little use.
The results were reported in a coordination meeting held in Seville, attended by about twenty collaborating scientists. From now on, specialists have to work to annotate the genome, finding where the genes are and identifying each of them, in order to complete this special "city map" of DNA. This is essential to make comparisons with other species and to study the evolution of the Iberian lynx, explained the project's coordinator, José Antonio Godoy.
The assembly has been a really challenging process that has required a greater effort than initially planned, and it has been led by the Genome Assembly and Annotation Team of the National Centre for Genome Analysis (CNAG), headed by Tyler Alioto, Andre Corvello.
The quality of the lynx genome reconstruction is high, approaching that of the cat's despite the substantially smallest cost of the former. The draft produced is very contiguous: more than half of the lynx genome is represented in fragments larger than 1.5 million bases. Moreover, another reliable indicator of assembly quality is to which extent common and easy to identify genes are fully or partially represented in the assembly. To evaluate this, scientist use a small number of genes that all species have in common, which are involved in cell essential processes like basic cellular metabolism or DNA replication. The lynx genome includes more than 95% of these basic genes, which is a good rate.
The first aim of this project is to build the genome of the species, using Candiles' DNA, a six year old male lynx from Andújar, in Andalusia. Additionally, samples from other eleven individuals, ten Iberian lynx and one European, has been sequenced but to a lesser extent. With the information of these additional genomes scientist can study the variation between different specimens to gain a clear picture of the Iberian lynx current genetic situation and to provide new tools to manage the existing populations with the goal of increasing its survival expectations.
For the lynx reference genome, the amount and type of sequence planned initially proved insufficient to achieve a minimum quality of assembly, so it was finally complemented using other strategies: with the sequencing of fragments of larger sizes and with the incorporation of a fosmid-pool sequencing approach.
At the end of this process, 'we have produced a high quality draft with a limited amount of sequencing effort and cost by applying novel approaches for genome sequencing and assembly, which may become of wider application to the whole genome shotgun of complex genomes', said Godoy.
The annotation phase will be a collaborative effort among different teams at the Centre of Genomic Regulation (CRG), leaded by Roderic Guigó and Cedric Notredame; the CNAG with Tyler Allioto's group, and the CNIO, were Alfonso Valencia is the head officer for this task.
The main aim of this research is to generate the first map of the Iberian lynx genome, which will provide important information on the evolution of this species and on the genetic consequences of its decline.
The lynx genomic sequence has already been identified by CNAG and is in the process of being assembled. When the process ends, in 2012, the researchers will face a new challenge: interpret it and compare it to other felid genomes.