Arboretum: Reconstruction and analysis of the evolutionary
history of condition-specific transcriptional modules
Sushmita Roy1,2,6,7, Ilan Wapinski1,3, Jenna Pfiffner1,
Courtney French1, Amanda Socha1, Jay Konieczka1, Naomi
Habib4, Manolis Kellis1,2, Dawn Thompson1 and Aviv
Regev1,5,7
Abstract
Comparative functional genomics studies the evolution of biological
processes by analyzing functional data, such as gene expression
profiles, across species. A major challenge is to compare profiles
collected in a complex phylogeny. Here, we present Arboretum, a
novel scalable computational algorithm that integrates expression
data from multiple species with species and gene phylogenies to
infer modules of coexpressed genes in extant species and their
evolutionary histories. We also develop new, generally applicable
measures of conservation and divergence in gene regulatory modules
to assess the impact of changes in gene content and expression on
module evolution. We used Arboretum to study the evolution of the
transcriptional response to heat shock in eight species of
Ascomycota fungi and to reconstruct modules of the ancestral
environmental stress response (ESR). We found substantial
conservation in the stress response across species and in the
reconstructed components of the ancestral ESR modules. The greatest
divergence was in the most induced stress, primarily through module
expansion. The divergence of the heat stress response exceeds that
observed in the response to glucose depletion in the same species.
Arboretum and its associated analyses provide a comprehensive
framework to systematically study regulatory evolution of
condition-specific responses.
http://genome.cshlp.org/content/23/6/1039.abstract
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Prof. Dr. Klaas Vandepoele
Tel. 32 (0)9 33 13822
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, Belgium
E-mail: Klaas.Vandepoele@psb.vib-ugent.be
Website: http://bioinformatics.psb.ugent.be/cig/
Twitter: http://twitter.com/plaza_genomics
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