The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of scientists brought together under the Biodiversity...

About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

About the 'ERGA iBOL Europe Connections' series The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of sc...

Last week, ERGA was present at the Vertebrate Genomes Project 2025 Conference, held at The Rockefeller University in New York City from September 30 and October 1. ERGA and VGP share a long-standing c...

YouTube video by ERGA - European Reference Genome Atlas

The European Reference Genome Atlas (ERGA) is a pan-European initiative that aims to facilitate the generation of high-quality reference genomes for the continent’s biodiversity as part of the g...

How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared gen...

29–31 October 2025Summary🗓️ Dates:  29 - 31 October 2025 (click to add to your agenda!)🔗 Online venue: ERGA YouTube ChannelWe are excited to announce the Genomics for Biodiversity Conference organised...

In June 2024, a dedicated team of seven researchers from various European institutions led by Rosalía Piñeiro, interim associate professor at the University of A Coruña (Spain), launched a conservatio...

Case study Culex mosquitoes Full genome sequencing can be crucial to understand how mosquitos spread diseases and how resistant they are to insecticides.  Learn more Analysing the genomic basis of vec...

In April 2024, the project “A new reference genome for the conservation of coastal species in the face of anthropogenic change” was selected in the ERGA-BGE call "Enhancing Biodiversity Genomics Appli...

The OrthoXML file is a standard file format for orthology data. It provides a standardized structure for describing orthologous and paralogous relationships while allowing the user to store custom and database-specific data in the same format. Although many orthology databases use it as a way to export data, there is no comprehensive toolkit for working with this format. Here, we introduce the OrthoXML-tools ( https://github.com/DessimozLab/orthoxml-tools ), a comprehensive toolkit for loading, manipulating, and exporting the OrthoXML files to other formats. We show its capabilities and performance on our benchmarks.

Orthologs are fundamental for enabling comparative genomics analyses that further our understanding of eukaryotic biology. The unprecedented increase in the availability of high-quality eukaryotic genomes necessitates scalable and accurate methods for orthology inference. The National Center for Biotechnology Information (NCBI) developed “NCBI Orthologs”, a resource and a computational pipeline designed to meet this challenge within the NCBI RefSeq framework. This system integrates protein similarity, nucleotide alignment, and microsynteny to achieve high-precision ortholog assignments across diverse eukaryotes. The pipeline leverages high-quality RefSeq annotations and processes genomes individually, ensuring scalability. Resulting ortholog data, organized into gene-level anchored sets, enables propagation of functional annotation information and facilitates comparative genomics. Critically, these data are integrated into the NCBI Gene resource, providing users with access from various entry points. The NCBI Datasets resource provides an intuitive interface to explore orthologous relationships on the web and allows bulk data download via the web, command-line tools, and an API. We detail the methodology, including anchor species selection and the decision tree used to arrive at high-confidence one-to-one orthology relationships. NCBI Orthologs is a valuable resource for facilitating functional annotation efforts and enhancing our understanding of eukaryotic gene evolution.