Co-locality to Co-functionality: Gene Neighborhoods and Fusions as a Tool for Gene Function Discovery

Event Sponsor: 
Data Science and Learning Candidate Presentation
Start Date: 
Jul 17 2019 - 1:00pm
Building/Room: 
Building 240/Room 4301
Location: 
Argonne National Laboratory
Speaker(s): 
Fatima Foflonker
Speaker(s) Title: 
Brookhaven National Laboratory
Host: 
Chris Henry

Sequence similarity based approaches alone to functional annotation of non-model organisms, which are distantly related to characterized model organisms, can be unreliable and inadequate. Algae represent one of the most diverse and complex groups, with over half of proteins of unknown function. Here, we utilize a comparative genomics approaches to infer protein function from physical associations, by identifying conserved gene neighborhoods and gene fusions in algae. Gene neighborhoods were defined as:  proximal orthologous genes within a 6 gene window, in a minimum of 4 species among ten green algae.  This resulted in 152 neighborhoods with potential functionally relevant neighborhoods including genes involved in carotenoid biosynthesis, photorespiration, nitrogen recycling, oxidative stress responses, and arsenic detoxification. Fusions were identified by searching for separate domains that were fused in one open reading frame among the algal species. Several genes of unknown function within neighborhoods were chosen to follow up with experimental characterization.