BACKGROUND: Models 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. RESULT: We 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. CONCLUSION: DeCoLT 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 complexes. AVAILABILITY: http://pbil.univ-lyon1.fr/software/DeCoLT/

Patterson, M., Szöllősi, G., Daubin, V., Tannier, E. (2013). Lateral Gene Transfer, Rearrangement, Reconciliation. BMC BIOINFORMATICS, 14(supplemento 15) [10.1186/1471-2105-14-S15-S4].

Lateral Gene Transfer, Rearrangement, Reconciliation

PATTERSON, MURRAY DAN
Primo
;
2013

Abstract

BACKGROUND: Models 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. RESULT: We 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. CONCLUSION: DeCoLT 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 complexes. AVAILABILITY: http://pbil.univ-lyon1.fr/software/DeCoLT/
Articolo in rivista - Articolo scientifico
Ancestral Gene Order Reconstruction, Lateral Gene Transfer, Species Tree Reconciliation, Dynamic Programming
English
2013
14
supplemento 15
S4
open
Patterson, M., Szöllősi, G., Daubin, V., Tannier, E. (2013). Lateral Gene Transfer, Rearrangement, Reconciliation. BMC BIOINFORMATICS, 14(supplemento 15) [10.1186/1471-2105-14-S15-S4].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/156388
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