  The architecture of eukaryotic coding genes allows the production of several
different protein isoforms by genes. Current gene phylogeny reconstruction
methods make use of a single protein product per gene, ignoring information on
alternative protein isoforms. These methods often lead to inaccurate gene tree
reconstructions that require to be corrected before being used in phylogenetic
tree reconciliation analyses or gene products phylogeny reconstructions. Here,
we propose a new approach for the reconstruction of accurate gene trees and
protein trees accounting for the production of alternative protein isoforms by
the genes of a gene family. We extend the concept of reconciliation to protein
trees, and we define a new reconciliation problem called MinDRGT that consists
in finding a gene tree that minimizes a double reconciliation cost with a given
protein tree and a given species tree. We define a second problem called
MinDRPGT that consists in finding a protein tree and a gene tree minimizing a
double reconciliation cost, given a species tree and a set of protein subtrees.
We provide algorithmic exact and heuristic solutions for some versions of the
problems, and we present the results of an application to the correction of
gene trees from the Ensembl database. An implementation of the heuristic method
is available at https://github.com/UdeS-CoBIUS/Protein2GeneTree.
