Evolclust: automated inference of evolutionary conserved gene clusters in eukaryotes

Marcet‐Houben, Marina; Gabaldón, Toni

doi:10.1101/698621

Cited by 2 publications

References 10 publications

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Quantifying Hierarchical Conflicts in Homology Statements

Swenson

Elghraoui

Valafar

et al. 2022

Comparative Genomics

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A fundamental step in any comparative whole genome analysis is the annotation of homology relationships between segments of the genomes. Traditionally, this annotation has been based on coding segments, where orthologous genes are inferred and then syntenic blocks are computed by agglomerating sets of homologous genes into homologous regions. More recently, whole genomes, including intergenic regions, are being aligned de novo as whole genome alignments (WGA). In this article we develop a test to measure to what extent sets of homology relationships given by two different software are hierarchically related to one another, where matched segments from one software may contain matched segments from the other and vice versa. Such a test should be used as a sanity check for an agglomerative syntenic block software, and provides a mapping between the blocks that can be used for further downstream analyses. We show that, in practice, it is rare that two collections of homology relationships are perfectly hierarchically related. Therefore we present an optimization problem to measure how far they are from being so. We show that this problem, which is a generalization of the assignment problem, is NP-Hard and give a heuristic solution and implementation. We apply our distance measure to data from the Alignathon competition, as well as to Mycobacterium tuberculosis, showing that many factors affect how hierarchically related two collections are, including sensitivities to guide trees and the use or omission of an outgroup. These findings inform practitioners on the pitfalls of homology relationship inference, and can inform development of more robust inference tools.

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Quantifying Hierarchical Conflicts in Homology Statements

Swenson

Elghraoui

Valafar

et al. 2022

Comparative Genomics

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Evolutionary and functional patterns of shared gene neighbourhood in fungi

Marcet‐Houben

Gabaldón

2019

Nat Microbiol

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Gene clusters comprise genomically co-localized and potentially co-regulated genes that tend to be conserved across species. In eukaryotes, multiple examples of metabolic gene clusters are known, particularly among fungi and plants. However, little is known about how gene clustering patterns vary among taxa, or among functional roles. Furthermore, mechanisms for the formation, maintenance and evolution of gene clusters remain a puzzle. We surveyed 341 fungal genomes to discover gene clusters shared by different species, independently of their functions. We inferred 12,120 cluster families, which comprised roughly one third of the gene space, and were enriched in diverse cellular functions. Additionally, most clusters did not encode transcription factors, suggesting they are regulated distally. We used phylogenomics to characterize the evolutionary history of these clusters. We found that most clusters originated once, and were transmitted vertically, coupled to differential loss. However, convergent 2 evolution -i.e. independent appearance of the same cluster-is more prevalent than anticipated.Finally, horizontal gene transfer of entire clusters was rather restricted, with the exception of secondary metabolism clusters. Altogether our results provide new insights on the evolution of gene clustering as well as a broad catalogue of evolutionarily conserved gene clusters whose function remains to be elucidated.

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Evolclust: automated inference of evolutionary conserved gene clusters in eukaryotes

Cited by 2 publications

References 10 publications

Quantifying Hierarchical Conflicts in Homology Statements

Quantifying Hierarchical Conflicts in Homology Statements

Evolutionary and functional patterns of shared gene neighbourhood in fungi

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