Gearing up to handle the mosaic nature of life in the quest for orthologs

Abstract

The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.

Fig. 1

Nested Evolutionary Histories: Containing (e.g. species) trees (grey area) with nested (e.g. gene) trees (red/blue) inside. Semicircles denote orthologous or orthology-like relations. On the top level (top left panel), subpopulations unique to a particular ecological niche are nested within populations, and within subpopulations in turn, the histories of individual genealogies are nested. In this sense, niche segregation within a site is a form of duplication event, whereas migration to novel habitats correspond to speciation events at this level. In addition, genes lie within genomes that are subject to whole-genome or chromosome-scale duplication events (top right panel, bottom left panel), which strongly influences genome evolution and involve discordances between the histories of components and wholes, and protein domains within genes may reshuffle over evolutionary time (bottom right panel), complicating the use of full-length sequences in orthology inference (Color version of this figure is available at Bioinformatics online.)