About the project

E-PAN aims to accelerate the use of pan-genome data in plant research by advancing data quality control, curation, integration and visualisation. While pan-genome sequencing and assembly are now well-established, the downstream integration and exploration of these data are held back by a lack of standards and tools.

The project focuses on gene-based comparative analysis of plant pan-genomes – particularly Presence Absence Variation (PAV) and structural rearrangements –across a selection of species important to agriculture and plant research: barley, potato, wheat, rice, and Arabidopsis.

E-PAN is led by ELIXIR Belgium (VIB), with partners across Germany, Portugal, Slovenia, and the UK.

ELIXIR-UK involvement

ELIXIR-UK Member, Rothamsted Research (KnetMiner spin-out) leads the project’s work on connecting and sharing pan-genome information across plant platforms. This includes prototyping data formats for exchanging pan-genome analysis results between platforms such as PLAZA/FRINGE and KnetMiner (two ELIXIR-UK endorsed services), and integrating new pan-genome information into KnetMiner’s knowledge graphs.

Rothamsted also contributes to community-building activities within the ELIXIR Plant Sciences Community.

Why it matters

Standardised quality control and data exchange for pan-genomes is currently a gap in the field, with researchers independently developing their own approaches. E-PAN’s outputs are expected to streamline pan-genome data submission into ELIXIR Core Data Resources such as ENA and Ensembl Genomes, and to benefit other ELIXIR Communities, including Galaxy and Biodiversity. Integration of new pan-genome data into platforms such as PLAZA and KnetMiner is expected to expand their reach across academia and industry.