Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes

Abstract

Phylogenetic profiling is a computational method to predict genes involved in the same biological process by identifying protein families which tend to be jointly lost or retained across the tree of life. Phylogenetic profiling has customarily been more widely used with prokaryotes than eukaryotes, because the method is thought to require many diverse genomes. There are now many eukaryotic genomes available, but these are considerably larger, and typical phylogenetic profiling methods require at least quadratic time as a function of the number of genes. We introduce a fast, scalable phylogenetic profiling approach entitled HogProf, which leverages hierarchical orthologous groups for the construction of large profiles and locality-sensitive hashing for efficient retrieval of similar profiles. We show that the approach outperforms Enhanced Phylogenetic Tree, a phylogeny-based method, and use the tool to reconstruct networks and query for interactors of the kinetochore complex as well as conserved proteins involved in sexual reproduction: Hap2, Spo11 and Gex1. HogProf enables large-scale phylogenetic profiling across the three domains of life, and will be useful to predict biological pathways among the hundreds of thousands of eukaryotic species that will become

Public good exploitation in natural bacterioplankton communities

“…Clusters of coevolving genes were first determined using the weighted minhash, using a low threshold (0.3) for similarity ( 33 ). Because of the low threshold and probabilistic nature of the minhash distance and resulting clustering, we then broke up clusters identified using the weighted minhash, as these clusters may contain illegitimately clustered vectors.…”

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

“…Thus, such co-evolution patterns can be used to infer functionally related genes—a technique known as ‘phylogenetic profiling’ ( 28 ). Recently, we introduced HogProf, an algorithm to efficiently identify similar HOGs in terms of their presence or absence at each extant and ancestral node in the genome taxonomy, as well as the duplication or loss events on the branch leading to that node ( 29 ). This functionality has been added to the OMA browser, making it possible, starting from any HOG, to identify similar HOGs using similar phylogenetic patterns.…”

“…Of note, the visual representation of the profile available on the web interface only shows the extant species covered by the query and returned HOGs. The actual profile similarities are calculated between the set of taxonomic nodes where ancestral presence was inferred along with extant species, as well as the set of ancestral duplications and losses shared between HOGs ( 29 ). Finally, phylogenetic profiles are also retrievable via the REST programmatic interface (under HOGs methods).…”

Inverse Potts model improves accuracy of phylogenetic profiling

“…Phylogenetic profiling is one such analysis method. In this method, when two ortholog groups (OGs) have similar occurrence patterns among species in a table of OGs, the two OGs are presumed to be functionally related ( Kensche et al , 2008 ; Moi et al , 2020 ; Niu et al , 2017 ; Pellegrini et al , 1999 ; Stupp et al , 2021 ; Tremblay et al , 2021 ; Tsaban et al , 2021 ). Although phylogenetic profiling was first proposed to detect protein–protein interactions, this method in principle captures any functional relationships between genes.…”

“…In other words, the conventional calculation of similarity introduces an evolutionary bias in the estimation. Therefore, methods that consider a phylogenetic tree were proposed and showed good performance ( Barker et al , 2007 ; Cohen et al , 2012 ; Moi et al , 2020 ; Ta et al , 2011 ; Vert, 2002 ).…”