Fractionation, rearrangement and subgenome dominance

David Sankoff,Chunfang Zheng

doi:10.1093/bioinformatics/bts392

Abstract

Motivation: Fractionation is arguably the greatest cause of gene order disruption following whole genome duplication, causing severe biases in chromosome rearrangement-based estimates of evolutionary divergence.Results: We show how to correct for this bias almost entirely by means of a ‘consolidation’ algorithm for detecting and suitably transforming identifiable regions of fractionation. We characterize the process of fractionation and the performance of the algorithm through realistic simulations. We apply our method to a number of core eudicot genomes, we and by studying the fractionation regions detected, are able to address topical issues in polyploid evolution.Availability and implementation: Code for the consolidation algorithm, and sample data, is available at: http://137.122.149.195/Software/Fractionation/fractionation.htmlContact: sankoff@uottawa.ca

Highlights

Fractionation [1], the loss of duplicate genes after whole genome duplication (WGD), causes more gene order disruption than classical chromosomal rearrangements such as inversion or reciprocal translocation
The consolidation algorithm was motivated as a way of correcting estimates of genomic divergence, but an important byproduct is its systematic identification of fractionation regions
An analytically advantageous feature of our analysis is that it partitions the rearrangements that have affected a tetraploid into those that have operated within a fractionation interval and those that have left these intervals intact, either because the intervals are outside the scope of the rearrangement or the interval is affected as a whole, without any effect internally

Summary

Introduction

Fractionation [1], the loss of duplicate genes after whole genome duplication (WGD), causes more gene order disruption than classical chromosomal rearrangements such as inversion or reciprocal translocation. Gene order disruption follows from the partly random choice of which of the two copies is deleted, i.e., which of two homeologous chromosomes retains the remaining single copy of the gene This process was first hypothesized by Wolfe and Shields in their 1997 demonstration of the ancient WGD of Saccharomyces cerevisiae [5], suggesting “... This is the result of random deletion of individual duplicated genes from one or other chromosome subsequent to the initial duplication of the whole region.” This loss pattern was further highlighted years later by the comparison of the S. cerevisiae gene order with that of related diploid yeasts by Dietrich et al [6] and Kellis et al [7], who called it “interleaving”, while Freeling was coining the usage “fractionation” in the context of plant genomics. This process was first hypothesized by Wolfe and Shields in their 1997 demonstration of the ancient WGD of Saccharomyces cerevisiae [5], suggesting “... this is the result of random deletion of individual duplicated genes from one or other chromosome subsequent to the initial duplication of the whole region.” This loss pattern was further highlighted years later by the comparison of the S. cerevisiae gene order with that of related diploid yeasts by Dietrich et al [6] and Kellis et al [7], who called it “interleaving”, while Freeling was coining the usage “fractionation” in the context of plant genomics.

Methods

Results

Conclusion