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GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryot...

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Autores principales: Lovell, John T, Sreedasyam, Avinash, Schranz, M Eric, Wilson, Melissa, Carlson, Joseph W, Harkess, Alex, Emms, David, Goodstein, David M, Schmutz, Jeremy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9462846/
https://www.ncbi.nlm.nih.gov/pubmed/36083267
http://dx.doi.org/10.7554/eLife.78526
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author Lovell, John T
Sreedasyam, Avinash
Schranz, M Eric
Wilson, Melissa
Carlson, Joseph W
Harkess, Alex
Emms, David
Goodstein, David M
Schmutz, Jeremy
author_facet Lovell, John T
Sreedasyam, Avinash
Schranz, M Eric
Wilson, Melissa
Carlson, Joseph W
Harkess, Alex
Emms, David
Goodstein, David M
Schmutz, Jeremy
author_sort Lovell, John T
collection PubMed
description The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.
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spelling pubmed-94628462022-09-10 GENESPACE tracks regions of interest and gene copy number variation across multiple genomes Lovell, John T Sreedasyam, Avinash Schranz, M Eric Wilson, Melissa Carlson, Joseph W Harkess, Alex Emms, David Goodstein, David M Schmutz, Jeremy eLife Evolutionary Biology The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes. eLife Sciences Publications, Ltd 2022-09-09 /pmc/articles/PMC9462846/ /pubmed/36083267 http://dx.doi.org/10.7554/eLife.78526 Text en © 2022, Lovell et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Evolutionary Biology
Lovell, John T
Sreedasyam, Avinash
Schranz, M Eric
Wilson, Melissa
Carlson, Joseph W
Harkess, Alex
Emms, David
Goodstein, David M
Schmutz, Jeremy
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
title GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
title_full GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
title_fullStr GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
title_full_unstemmed GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
title_short GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
title_sort genespace tracks regions of interest and gene copy number variation across multiple genomes
topic Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9462846/
https://www.ncbi.nlm.nih.gov/pubmed/36083267
http://dx.doi.org/10.7554/eLife.78526
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