License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2022.5
URN: urn:nbn:de:0030-drops-170390
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2022/17039/
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Gascon, Mathieu ; El-Mabrouk, Nadia

Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer

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Abstract

Gene transfer between the mitochondrial and nuclear genome of the same species, called endosymbiotic gene transfer (EGT), is a mechanism which has largely shaped gene contents in eukaryotes since a unique ancestral endosymbiotic event know to be at the origin of all mitochondria. The gene tree-species tree reconciliation model has been recently extended to account for EGTs: given a binary gene tree and a binary species tree, the EndoRex software outputs an optimal DLE-Reconciliation, that is an embedding of the gene tree into the species tree inducing a most parsimonious history of Duplications, Losses and EGT events. Here, we provide the first algorithmic study for DLE-Reconciliation in the case of a multifurcated (non-binary) gene tree. We present a general two-steps method: first, ignoring the mitochondrial-nuclear (or 0-1) labeling of leaves, output a binary resolution minimizing the DL-Reconciliation and, for each resolution, assign a known number of 0s and 1s to the leaves in a way minimizing EGT events. While Step 1 corresponds to the well studied non-binary DL-Reconciliation problem, the complexity of the formal label assignment problem related to Step 2 is unknown. Here, we show it is NP-complete even for a single polytomy (non-binary node). We then provide a heuristic which is exact for the unitary cost of operations, and a polynomial-time algorithm for solving a polytomy in the special case where genes are specific to a single genome (mitochondrial or nuclear) in all but one species.

BibTeX - Entry

@InProceedings{gascon_et_al:LIPIcs.WABI.2022.5,
  author =	{Gascon, Mathieu and El-Mabrouk, Nadia},
  title =	{{Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{5:1--5:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2022/17039},
  URN =		{urn:nbn:de:0030-drops-170390},
  doi =		{10.4230/LIPIcs.WABI.2022.5},
  annote =	{Keywords: Reconciliation, Duplication, Endosymbiotic gene transfer, Multifurcated gene tree, Polytomy}
}

Keywords: Reconciliation, Duplication, Endosymbiotic gene transfer, Multifurcated gene tree, Polytomy
Collection: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Issue Date: 2022
Date of publication: 26.08.2022

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