Cargando…
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...
Autores principales: | , , , , , , , , |
---|---|
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 |
_version_ | 1784787281845944320 |
---|---|
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. |
format | Online Article Text |
id | pubmed-9462846 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT lovelljohnt genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT sreedasyamavinash genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT schranzmeric genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT wilsonmelissa genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT carlsonjosephw genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT harkessalex genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT emmsdavid genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT goodsteindavidm genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes AT schmutzjeremy genespacetracksregionsofinterestandgenecopynumbervariationacrossmultiplegenomes |