Automatic genome-wide reconstruction of phylogenetic gene trees

Wapinski, Ilan; Pfeffer, Avi; Friedman, Nir; Regev, Aviv

doi:10.1093/bioinformatics/btm193

Cited by 127 publications

(126 citation statements)

References 26 publications

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“…We ran Arboretum on expression data measuring the heat shock response of eight species using orthology mappings from the Synergy algorithm (http://www.broadinstitute.org/regev/orthogroups/) (Wapinski et al 2007a). The strains, growth conditions, microarray hybridization, and data preprocessing are described in detail in the Supplemental Methods, and microrray data are available at GSE38478.…”

Section: Analysis Of Heat Shock Response In Eight Speciesmentioning

confidence: 99%

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

et al. 2013

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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.

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Section: Analysis Of Heat Shock Response In Eight Speciesmentioning

confidence: 99%

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

et al. 2013

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“…Ortholog prediction and alignment: Annotated Saccharomyces cerevisiae, S. paradoxus, S. mikatae, and S. bayanus protein sequences were obtained from the Saccharomyces Genome Database (accessed January 2008; http:/ / www.yeastgenome.org/) (Goffeau et al 1996;Kellis et al 2003 Orthology assignments within yeast, Drosophila, and mammals were obtained using the SYNERGY algorithm (Wapinski et al 2007). Briefly, SYNERGY performs a bottom-up traversal of a species tree, identifying orthologs between the species below each ancestral species in the tree.…”

Section: Methodsmentioning

confidence: 99%

Overdispersion of the Molecular Clock Varies Between Yeast, Drosophila and Mammals

2008

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Although protein evolution can be approximated as a ''molecular evolutionary clock,'' it is well known that sequence change departs from a clock-like Poisson expectation. Through studying the deviations from a molecular clock, insight can be gained into the forces shaping evolution at the level of proteins. Generally, substitution patterns that show greater variance than the Poisson expectation are said to be ''overdispersed.'' Overdispersion of sequence change may result from temporal variation in the rate at which amino acid substitutions occur on a phylogeny. By comparing the genomes of four species of yeast, five species of Drosophila, and five species of mammals, we show that the extent of overdispersion shows a strong negative correlation with the effective population size of these organisms. Yeast proteins show very little overdispersion, while mammalian proteins show substantial overdispersion. Additionally, X-linked genes, which have reduced effective population size, have gene products that show increased overdispersion in both Drosophila and mammals. Our research suggests that mutational robustness is more pervasive in organisms with large population sizes and that robustness acts to stabilize the molecular evolutionary clock of sequence change.

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“…Very few studies use synteny information to construct gene trees. The only ones we are aware of are the ones of Wapinski et al [75,76]. In these papers, family clustering as well as gene trees are constructed with a "synteny score" as well as a "sequence score".…”

Section: Synteny Informs Gene Family Evolutionmentioning

confidence: 99%

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

Chauve

El-Mabrouk

Guéguen

et al. 2013

Models and Algorithms for Genome Evolution

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Abstract. The evolution of genomes can be studied at at least three different scales: the nucleotide level, accounting for substitutions and indels, the gene level, accounting for gains and losses, and the genome level, accounting for rearrangements of chromosome organization. While the nucleotide and gene levels are now often integrated in a single model using reconciled gene trees, very little work integrates the genome level as well, and considers gene trees and gene orders simultaneously. In a seminal book chapter published in 2000 and entitled "Duplication, Rearrangement and Reconciliation", Sankoff and El-Mabrouk outlined a general approach, making a step in that direction. This avenue has been poorly exploited by the community for over ten years, but recent developments allow the design of integrated methods where phylogeny informs the study of synteny and vice-versa. We review these developments and show how this influence of synteny on gene tree construction can be implemented.

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Automatic genome-wide reconstruction of phylogenetic gene trees

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 127 publications

References 26 publications

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

Overdispersion of the Molecular Clock Varies Between Yeast, Drosophila and Mammals

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

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