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Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families
MOTIVATION: Reconstruction of gene copy number evolution is an essential approach for understanding how complex biological systems have been organized. Although various models have been proposed for gene copy number evolution, existing evolutionary models have not appropriately addressed the fact th...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9710636/ https://www.ncbi.nlm.nih.gov/pubmed/36700099 http://dx.doi.org/10.1093/bioadv/vbab014 |
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author | Fukunaga, Tsukasa Iwasaki, Wataru |
author_facet | Fukunaga, Tsukasa Iwasaki, Wataru |
author_sort | Fukunaga, Tsukasa |
collection | PubMed |
description | MOTIVATION: Reconstruction of gene copy number evolution is an essential approach for understanding how complex biological systems have been organized. Although various models have been proposed for gene copy number evolution, existing evolutionary models have not appropriately addressed the fact that different gene families can have very different gene gain/loss rates. RESULTS: In this study, we developed Mirage (MIxtuRe model for Ancestral Genome Estimation), which allows different gene families to have flexible gene gain/loss rates. Mirage can use three models for formulating heterogeneous evolution among gene families: the discretized Γ model, probability distribution-free model and pattern mixture (PM) model. Simulation analysis showed that Mirage can accurately estimate heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that the PM model fits genome data from various taxonomic groups better than the other heterogeneous models. Using Mirage, we revealed that metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated. AVAILABILITY AND IMPLEMENTATION: The source code of Mirage is freely available at https://github.com/fukunagatsu/Mirage. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online. |
format | Online Article Text |
id | pubmed-9710636 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-97106362023-01-24 Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families Fukunaga, Tsukasa Iwasaki, Wataru Bioinform Adv Original Article MOTIVATION: Reconstruction of gene copy number evolution is an essential approach for understanding how complex biological systems have been organized. Although various models have been proposed for gene copy number evolution, existing evolutionary models have not appropriately addressed the fact that different gene families can have very different gene gain/loss rates. RESULTS: In this study, we developed Mirage (MIxtuRe model for Ancestral Genome Estimation), which allows different gene families to have flexible gene gain/loss rates. Mirage can use three models for formulating heterogeneous evolution among gene families: the discretized Γ model, probability distribution-free model and pattern mixture (PM) model. Simulation analysis showed that Mirage can accurately estimate heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that the PM model fits genome data from various taxonomic groups better than the other heterogeneous models. Using Mirage, we revealed that metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated. AVAILABILITY AND IMPLEMENTATION: The source code of Mirage is freely available at https://github.com/fukunagatsu/Mirage. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online. Oxford University Press 2021-07-30 /pmc/articles/PMC9710636/ /pubmed/36700099 http://dx.doi.org/10.1093/bioadv/vbab014 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Fukunaga, Tsukasa Iwasaki, Wataru Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families |
title | Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families |
title_full | Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families |
title_fullStr | Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families |
title_full_unstemmed | Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families |
title_short | Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families |
title_sort | mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9710636/ https://www.ncbi.nlm.nih.gov/pubmed/36700099 http://dx.doi.org/10.1093/bioadv/vbab014 |
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