» Articles » PMID: 32508979

Evolution Through Segmental Duplications and Losses: a Super-Reconciliation Approach

Overview
Publisher Biomed Central
Date 2020 Jun 9
PMID 32508979
Citations 7
Authors
Affiliations
Soon will be listed here.
Abstract

The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the problem which consists in inferring a history of segmental duplication and loss events (involving a set of neighboring genes) leading to a set of present-day syntenies from a single ancestral one. In other words, we extend the traditional Duplication-Loss reconciliation problem of a single gene tree, to a set of trees, accounting for segmental duplications and losses. Existency of a Super-Reconciliation depends on individual gene tree consistency. In addition, ignoring rearrangements implies that existency also depends on gene order consistency. We first show that the problem of reconstructing a most parsimonious Super-Reconciliation, if any, is NP-hard and give an exact exponential-time algorithm to solve it. Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm. We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes.

Citing Articles

Genome-wide patterns of homoeologous gene flow in allotetraploid coffee.

Ortiz A, Sharbrough J Appl Plant Sci. 2024; 12(4):e11584.

PMID: 39184198 PMC: 11342229. DOI: 10.1002/aps3.11584.


Predicting horizontal gene transfers with perfect transfer networks.

Lopez Sanchez A, Lafond M Algorithms Mol Biol. 2024; 19(1):6.

PMID: 38321476 PMC: 10848447. DOI: 10.1186/s13015-023-00242-2.


Molecular evolution and diversification of phytoene synthase (PSY) gene family.

Lisboa M, Canal D, Filgueiras J, Turchetto-Zolet A Genet Mol Biol. 2022; 45(4):e20210411.

PMID: 36537743 PMC: 9764326. DOI: 10.1590/1678-4685-GMB-2021-0411.


WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events.

Henry C, Piper K, Wilson A, Miraszek J, Probst C, Rong Y BMC Bioinformatics. 2022; 23(1):505.

PMID: 36434497 PMC: 9701042. DOI: 10.1186/s12859-022-05042-w.


Maximum parsimony reconciliation in the DTLOR model.

Liu J, Mawhorter R, Liu N, Santichaivekin S, Bush E, Libeskind-Hadas R BMC Bioinformatics. 2021; 22(Suppl 10):394.

PMID: 34348661 PMC: 8340394. DOI: 10.1186/s12859-021-04290-6.


References
1.
Ma J, Zhang L, Suh B, Raney B, Burhans R, Kent W . Reconstructing contiguous regions of an ancestral genome. Genome Res. 2006; 16(12):1557-65. PMC: 1665639. DOI: 10.1101/gr.5383506. View

2.
Hafeez M, Shabbir M, Altaf F, Abbasi A . Phylogenomic analysis reveals ancient segmental duplications in the human genome. Mol Phylogenet Evol. 2015; 94(Pt A):95-100. DOI: 10.1016/j.ympev.2015.08.019. View

3.
Tofigh A, Hallett M, Lagergren J . Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans Comput Biol Bioinform. 2011; 8(2):517-35. DOI: 10.1109/TCBB.2010.14. View

4.
Bansal M, Burleigh J, Eulenstein O, Fernandez-Baca D . Robinson-Foulds supertrees. Algorithms Mol Biol. 2010; 5:18. PMC: 2846952. DOI: 10.1186/1748-7188-5-18. View

5.
Lafond M, Ouangraoua A, El-Mabrouk N . Reconstructing a SuperGeneTree minimizing reconciliation. BMC Bioinformatics. 2015; 16 Suppl 14:S4. PMC: 4602317. DOI: 10.1186/1471-2105-16-S14-S4. View