Orthology detection strategies for improved phylogenetic profiling and functional annotation of plant genomes

General info

Date from - to

01 Nov 2009 - 01 Nov 2012

Project leader(s)

Leunissen, Jack Prof. dr.

Abstract

Aim of the project:
Develop and apply orthology detection and phylogenetic profiling methods for
improved function annotation of plant genomes. 

Key objectives:

• Developing improved strategies for function annotation of plant genomes;
• Studying protein or gene families and metabolic pathways using improved ortholog clustering and phylogenetic profiling methods.

Approach:
The project starts with the application and assessment of orthology detection methods as well as novel hierarchical clustering approaches on all currently available plant proteomes. We will then evaluate methods which combine orthology predictions with auxiliary (genome-context) data obtained from high-throughput experiments including protein-protein interactions, gene expression data, and (micro-) synteny. For the latter we will use multigenome alignment methods to predict and analyse syntenic regions across plant genomes of  wide  evolutionary distances, from the ~400 million year divergence between mosses and flowering plants to the ~12 million year divergence between tomato and potato. The resulting orthology predictions will subsequently be used in phylogenetic profiling to improve plant genome annotations and to provide a basis for detailed analysis of particular gene families and metabolic pathways in tomato and potato (priority species of the Centre for BioSystems Genomics, CBSG) and Brassicaceae model species.

Publications

• Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks
• Evidence for RNA recombination between distinct isolates of Pepino mosaic virus