Xenolog classification

Abstract

MotivationOrthology analysis is a fundamental tool in comparative genomics. Sophisticated methods have been developed to distinguish between orthologs and paralogs and to classify paralogs into subtypes depending on the duplication mechanism and timing, relative to speciation. However, no comparable framework exists for xenologs: gene pairs whose history, since their divergence, includes a horizontal transfer. Further, the diversity of gene pairs that meet this broad definition calls for classification of xenologs with similar properties into subtypes.ResultsWe present a xenolog classification that uses phylogenetic reconciliation to assign each pair of genes to a class based on the event responsible for their divergence and the historical association between genes and species. Our classes distinguish between genes related through transfer alone and genes related through duplication and transfer. Further, they separate closely-related genes in distantly-related species from distantly-related genes in closely-related species. We present formal rules that assign gene pairs to specific xenolog classes, given a reconciled gene tree with an arbitrary number of duplications and transfers. These xenology classification rules have been implemented in software and tested on a collection of ∼13 000 prokaryotic gene families. In addition, we present a case study demonstrating the connection between xenolog classification and gene function prediction.Availability and ImplementationThe xenolog classification rules have been implemented in Notung 2.9, a freely available phylogenetic reconciliation software package. http://www.cs.cmu.edu/~durand/Notung. Gene trees are available at http://dx.doi.org/10.7488/ds/1503.Supplementary information Supplementary data are available at Bioinformatics online.

Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

“…Gene tree reconstructions were performed in RAxML under the PROTGAMMAWAG model with 100 rapid bootstrap replicates. Gene trees were rerooted and reconciled with the species tree using Notung 2.9 ( 80 ) with 80% bootstrap support as the edge-weight threshold for topological rearrangements. After ortholog coding, duplications and losses for each orthogroup were mapped onto the species tree using Dollo parsimony ( 43 ).…”

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

“…Third party software parameters MAFFT (v6.861) [17] was used with default parameters (-auto) and -memsave when the input sequence was above 4000 amino acids; FastTree (v2.1.9) [18] with -nopr -pseudo -mlacc 3 -slownni options for increased reconstruction accuracy; NOTUNG (v2.9) [24] with default weighing scheme (D=1.5, L=1) and therearrange option with threshold 0.9. The latter option rearranges the topology of the tree for weakly supported branches to minimize the cumulative cost of the reconciliation.…”

Evidence for parallel evolution of a gene involved in the regulation of spermatogenesis

“…This could be due to greater sequence divergence in this protein family and the paucity of additional family members in various sections of the evolutionary tree. To obtain a tree that is more likely to approximate the evolutionary events that gave rise to this family of proteins, we used Notung-2.9 [15] to first reconcile the two trees with the current species tree (NCBI) and subsequently rearrange the trees based on parsimony. With both the neighbour-joining and maximum-likelihood methods, this resulted in single optimal trees that are very similar (neighbour-joining, figure 2, maximum-likelihood, electronic supplementary material, figure S2).…”