David Sankoff1, Chunfang Zheng. 1. Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5. sankoff@uottawa.ca
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.html CONTACT: sankoff@uottawa.ca.
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.html CONTACT: sankoff@uottawa.ca.
Authors: Douglas E Soltis; Victor A Albert; Jim Leebens-Mack; Charles D Bell; Andrew H Paterson; Chunfang Zheng; David Sankoff; Claude W Depamphilis; P Kerr Wall; Pamela S Soltis Journal: Am J Bot Date: 2009-01 Impact factor: 3.844
Authors: Fred S Dietrich; Sylvia Voegeli; Sophie Brachat; Anita Lerch; Krista Gates; Sabine Steiner; Christine Mohr; Rainer Pöhlmann; Philippe Luedi; Sangdun Choi; Rod A Wing; Albert Flavier; Thomas D Gaffney; Peter Philippsen Journal: Science Date: 2004-03-04 Impact factor: 47.728
Authors: Gavin M Douglas; Gesseca Gos; Kim A Steige; Adriana Salcedo; Karl Holm; Emily B Josephs; Ramesh Arunkumar; J Arvid Ågren; Khaled M Hazzouri; Wei Wang; Adrian E Platts; Robert J Williamson; Barbara Neuffer; Martin Lascoux; Tanja Slotte; Stephen I Wright Journal: Proc Natl Acad Sci U S A Date: 2015-02-17 Impact factor: 11.205