Thanks to the recent advances in sequencing technologies and bioinformatics, the field of genomics has entered the era of ambitious projects such as the Earth BioGenome, aiming to decode the genomic information of all living organisms. Along with the vast impact these efforts will have on science and society, there is now an unprecedented demand for the technical resources and protocols needed to handle, share, and explore the resulting data. While ELIXIR-CZ activities in genomics reflect major trends and challenges in the field, the consortium is aware of the risk of diluting its efforts should it aim to cover the full breadth of the discipline. Instead, it will focus on supporting the selected research areas outlined below that have a long tradition of excellent research work and an active scientific community in the Czech Republic.
Key domains and services in ELIXIR CZ are:
- Annotation of repetitive DNA elements in eukaryotic genomes. There are ongoing activities to develop and make publicly accessible various computational tools for identifying and annotating repetitive DNA elements in genome assemblies or next-generation sequencing reads (RepeatExplorer, TAREAN, and DANTE pipelines). Reference databases of repetitive DNA include, for example, the database of mobile element protein domains (REXdb) or human endogenous retrovirus database (HERVd).
- Phylogenomics and barcoding. The utilization of large-scale genomic data for resolving phylogenetic relationships between organisms and populations is a powerful application of genomics. Together with DNA barcoding, it has many applications in evolutionary biology, taxonomy, conservation biology, population genomics and epidemiology. Current activities include the development of the AmtDB database.
- Genomics of selected groups of organisms, including parasitic protists, neglected crop species, and fungal and microbial communities. These organisms are traditionally of strong interest to the genomics community in the Czech Republic, resulting in substantial data resources and expertise being developed over the last few years (e.g., the GlobalFungi database).
The following goals are proposed to promote further development and to deal with the major challenges of genomic research in the key domains listed above. They address two broad categories of researchers: those involved in the development of bioinformatics tools and the generation of data resources, and those who are mainly users of these resources. Each of these groups faces different challenges, the former mainly due to limitations in terms of computational resources, while the latter is primarily concerned with difficulties in using the tools or accessing genomic data with a limited knowledge of (bio)informatics.
Challenges and goals of ELIXIR CZ
- Goal 1: Promote the establishment of novel computational tools and databases by providing computational and data storage capacities to the Czech research community involved in their development. Facilitate the integration of these tools into international infrastructures.
- Goal 2: Support genomic projects by providing hardware resources for the exponentially growing amounts of biological data and expertise for making this data publicly available (interoperability, FAIRification).
- Goal 3: Provide user-friendly access to the supported computational tools and databases for researchers who are not trained in bioinformatics. Support containerization of the tools to promote reproducible execution. Organize practical training in using the tools.