Reconstruction of ancestral gene orders using intermediate genomes.

Pedro Feijão

doi:10.1186/1471-2105-16-s14-s3

Abstract

BackgroundThe problem of reconstructing ancestral genomes in a given phylogenetic tree arises in many different comparative genomics fields. Here, we focus on reconstructing the gene order of ancestral genomes, a problem that has been largely studied in the past 20 years, especially with the increasing availability of whole genome DNA sequences. There are two main approaches to this problem: event-based methods, that try to find the ancestral genomes that minimize the number of rearrangement events in the tree; and homology-based, that look for conserved structures, such as adjacent genes in the extant genomes, to build the ancestral genomes.ResultsWe propose algorithms that use the concept of intermediate genomes, arising in optimal pairwise rearrangement scenarios. We show that intermediate genomes have combinatorial properties that make them easy to reconstruct, and develop fast algorithms with better reconstructed ancestral genomes than current event-based methods. The proposed framework is also designed to accept extra information, such as results from homology-based approaches, giving rise to combined algorithms with better results than the original methods.

Highlights

The problem of reconstructing ancestral genomes in a given phylogenetic tree arises in many different comparative genomics fields
The proposed algorithms were implemented in Python and tested on simulated datasets, where a tree with genomes at the leaves is given as input, and the algorithms try to reconstruct the ancestral genomes at internal nodes of the tree
ProCARs was chosen because it was the easiest of the homology methods to run, and according to its authors it has similar results when compared to ANGES, InferCARs and GapAdj [14]

Summary

Introduction

The problem of reconstructing ancestral genomes in a given phylogenetic tree arises in many different comparative genomics fields. We focus on reconstructing the gene order of ancestral genomes, a problem that has been largely studied in the past 20 years, especially with the increasing availability of whole genome DNA sequences. Reconstructing ancestral genomes based on gene order data is an important problem that has been largely studied in the past years, especially with the increasing availability of whole genome DNA sequences. This problem, called the small parsimony problem, receives as input a phylogenetic tree with extant genomes at its leaves, and asks for the reconstructed gene orders at the internal nodes of the tree, corresponding to ancestral genomes. Since rearrangement distance problems are usually NP-hard for three or more genomes, these methods tend to be time consuming, especially when exact solutions are implemented

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Discussion

Conclusion