Resolution effects in reconstructing ancestral genomes

BACKGROUND: The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. RESULTS: We use the median reconstruction at the synteny block level, of th...

Descripción completa

Detalles Bibliográficos
Autores principales: Zheng, Chunfang, Jeong, Yuji, Turcotte, Madisyn Gabrielle, Sankoff, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Research
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954274/
https://www.ncbi.nlm.nih.gov/pubmed/29764371
http://dx.doi.org/10.1186/s12864-018-4462-y
_version_ 1783323488147210240
author Zheng, Chunfang
Jeong, Yuji
Turcotte, Madisyn Gabrielle
Sankoff, David
author_facet Zheng, Chunfang
Jeong, Yuji
Turcotte, Madisyn Gabrielle
Sankoff, David
author_sort Zheng, Chunfang
collection PubMed
description BACKGROUND: The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. RESULTS: We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. CONCLUSIONS: We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.
format Online
Article
Text
id pubmed-5954274
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-59542742018-05-21 Resolution effects in reconstructing ancestral genomes Zheng, Chunfang Jeong, Yuji Turcotte, Madisyn Gabrielle Sankoff, David BMC Genomics Research BACKGROUND: The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. RESULTS: We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. CONCLUSIONS: We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics. BioMed Central 2018-05-09 /pmc/articles/PMC5954274/ /pubmed/29764371 http://dx.doi.org/10.1186/s12864-018-4462-y Text en © The Author(s) 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Zheng, Chunfang
Jeong, Yuji
Turcotte, Madisyn Gabrielle
Sankoff, David
Resolution effects in reconstructing ancestral genomes
title Resolution effects in reconstructing ancestral genomes
title_full Resolution effects in reconstructing ancestral genomes
title_fullStr Resolution effects in reconstructing ancestral genomes
title_full_unstemmed Resolution effects in reconstructing ancestral genomes
title_short Resolution effects in reconstructing ancestral genomes
title_sort resolution effects in reconstructing ancestral genomes
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954274/
https://www.ncbi.nlm.nih.gov/pubmed/29764371
http://dx.doi.org/10.1186/s12864-018-4462-y
work_keys_str_mv AT zhengchunfang resolutioneffectsinreconstructingancestralgenomes
AT jeongyuji resolutioneffectsinreconstructingancestralgenomes
AT turcottemadisyngabrielle resolutioneffectsinreconstructingancestralgenomes
AT sankoffdavid resolutioneffectsinreconstructingancestralgenomes

Ejemplares similares