Oct 28, 2014

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation

BioRxiv : the Preprint Server for Biology
Nengyi ZhangEdward Buckler

Abstract

Horizontal gene transfer is one of the most important mechanisms for microbial evolution and adaptation. It is well known that horizontal gene transfer can be either 'additive' or 'replacing' depending on whether the transferred gene adds itself as a new gene in the recipient genome or replaces an existing homologous gene. Yet, all existing phylogenetic techniques for the inference of horizontal gene transfer assume either that all transfers are additive or that all transfers are replacing. This limitation not only affects the applicability and accuracy of these methods but also makes it difficult to distinguish between additive and replacing transfers. Here, we address this important problem by formalizing a phylogenetic reconciliation framework that simultaneously models both additive and replacing transfer events. Specifically, we (1) introduce the DTRL reconciliation framework that explicitly models both additive and replacing transfer events, along with gene duplications and losses, (2) prove that the underlying computational problem is NP-hard, (3) perform the first experimental study to assess the impact of replacing transfer events on the accuracy of the traditional DTL reconciliation model (which assumes that all trans...Continue Reading

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Mentioned in this Paper

Metabolic Process, Cellular
Genome-Wide Association Study
Study
Nitrogen Metabolism Pathway
Genes
Genetic Pleiotropy
Zea mays
Carbon
Metabolic Syndrome Pathway
Genomics

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