A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometime...

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Autores principales:	Cedric Chauve, Eric Tannier
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c94342e4fde043e082d10a23b58149c6
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spelling	oai:doaj.org-article:c94342e4fde043e082d10a23b58149c62021-11-25T05:41:57ZA methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.1553-734X1553-735810.1371/journal.pcbi.1000234https://doaj.org/article/c94342e4fde043e082d10a23b58149c62008-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19043541/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data acquisition.Cedric ChauveEric TannierPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 11, p e1000234 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Cedric Chauve Eric Tannier A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
description	The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data acquisition.
format	article
author	Cedric Chauve Eric Tannier
author_facet	Cedric Chauve Eric Tannier
author_sort	Cedric Chauve
title	A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
title_short	A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
title_full	A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
title_fullStr	A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
title_full_unstemmed	A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
title_sort	methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/c94342e4fde043e082d10a23b58149c6
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A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

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