Lateral gene transfer, rearrangement, reconciliationReport as inadecuate

Lateral gene transfer, rearrangement, reconciliation - Download this document for free, or read online. Document in PDF available to download.

* Corresponding author 1 BEAGLE - Artificial Evolution and Computational Biology LIRIS - Laboratoire d-InfoRmatique en Image et Systèmes d-information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive, CarMeN - Laboratoire de recherche en cardiovasculaire, métabolisme, diabétologie et nutrition 2 LBBE - Laboratoire de Biométrie et Biologie Evolutive 3 ELTE-MTA -Lendület- Biophysics Research Group Budapest

Abstract : BackgroundModels of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. These models have so far ignored lateral gene transfer, even though in unicellular organisms it can have an important confounding effect, and can be a rich source of information on the function of genes through the detection of transfers of clusters of genes.ResultWe report an algorithm together with its implementation, DeCoLT, that reconstructs ancestral genome organization based on reconciled gene trees which summarize information on sequence evolution, gene origination, duplication, loss, and lateral transfer. DeCoLT optimizes in polynomial time on the number of rearrangements, computed as the number of gains and breakages of adjacencies between pairs of genes. We apply DeCoLT to 1099 gene families from 36 cyanobacteria genomes.ConclusionDeCoLT is able to reconstruct adjacencies in 35 ancestral bacterial genomes with a thousand gene families in a few hours, and detects clusters of co-transferred genes. DeCoLT may also be used with any relationship between genes instead of adjacencies, to reconstruct ancestral interactions, functions or

Author: Murray Patterson - Gergely Szöllősi - Vincent Daubin - Eric Tannier -



Related documents