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2017 ; 33
(5
): 640-649
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Xenolog classification
#MMPMID27998934
Darby CA
; Stolzer M
; Ropp PJ
; Barker D
; Durand D
Bioinformatics
2017[Mar]; 33
(5
): 640-649
PMID27998934
show ga
MOTIVATION: Orthology 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. RESULTS: We 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
IMPLEMENTATION: The xenolog classification rules have been implemented in N otung
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 . CONTACT: durand@cmu.edu. SUPPLEMENTARY
INFORMATION: Supplementary data are available at Bioinformatics online.
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