Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration
Sina Majidian, Armin Hadziahmetovic, Felix Langschied, Stefano Pascarelli, Silvia Prieto-Baños, Jorge Rojas-Vargas, Lars Arvestad, Jitender Cheema, Salvatore Cosentino, Ingo Ebersberger, Elena Kuzmin, Yannis Nevers, Nikolai Romashchenko, Maureen Stolzer, Yan Wang, Alex Warwick Vesztrocy, Y. Xiao, Edward L. Braun, Christophe Dessimoz, Abdoulaye Baniré Diallo, Dannie Durand, Gang Fang, Toni Gabaldón, Natasha Glover, David A. Liberles, Claire D. McWhite, Erik L. L. Sonnhammer, Paul D. Thomas, Aïda Ouangraoua, Irene Julca
Abstract
The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthology plays a crucial role in understanding evolutionary patterns of genes and their functions. At the last Quest for Orthologs meeting (Montréal, Canada-2024), we discussed recent advances in orthology inference, with a focus on the impact of artificial intelligence (AI), protein structures, RNA splicing isoforms, and protein domain evolution together with other evolutionary considerations. A long-standing challenge in the field is the functional annotation of paralogs, for which we present novel approaches. The meeting also emphasised strategies for integrating diverse genetic features into the concept of orthology, encouraging frameworks that account for elements like alternative splicing, domain organisation, and regulatory sequences. We discuss various applications of orthology and paralogy to environmental research, agriculture, and comparative genomics. Additionally, we report recent progress in orthology inference methodologies and resources. This work represents a collaborative synthesis of insights and innovations presented at the 8th Quest for Orthologs meeting, highlighting current progress while outlining future directions for orthology research.