The work of the Computational Biology Unit of FEM in the field of genomics is focused on De Novo genome assembly, as well as on the analysis of re-sequencing data, using the latest DNA sequencing
technologies available. We are also active in downstream data interpretation and develop methods and pipelines for functional annotation of assembled genomes.
Genomics at FEM has a long and established history that dates back to the release of the grapevine (Vitis Vinifera - 2007) and apple (Malus x Domestica Borkh - 2010) high-quality draft genome sequences done almost entirely with Sanger sequencing, to the more recent assembly of the apple (cv. Golden Delicious) double haploid genome (2017), built by integrating Illumina, PacBio and BioNano data.
These projects made the Computational Biology Unit acquire an extensive experience in dealing with the peculiarities of plant genomes and allowed it to actively take part in the sequencing projects of strawberry, pear and peach.
Alongside genome assembly, we effectively used the team's competence to develop methods and pipelines to perform various bioinformatics analysis. Some examples are the design of tools to investigate the genetic diversity of crops, like the medium (20K Illumina Infinium) and high-density (Apple480K Affymetrix Axiom) apple SNP arrays that we produced within the FuitBreedomcis European project (http://www.fruitbreedomics.com/ ), or genotyping data analysis software like ASSIsT: the automated SNP scoring tool.
Genome functional annotation is another field of activity of the group in which data integration among different sources plays a major role. In this context, we developed Argot, an automated functional annotation pipeline that was ranked in the top 10 at the first two CAFA editions.