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Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants

We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how muc...

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Autores principales: Yu, Zhe, Zheng, Chunfang, Albert, Victor A., Sankoff, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775554/
https://www.ncbi.nlm.nih.gov/pubmed/33391353
http://dx.doi.org/10.3389/fgene.2020.603056
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author Yu, Zhe
Zheng, Chunfang
Albert, Victor A.
Sankoff, David
author_facet Yu, Zhe
Zheng, Chunfang
Albert, Victor A.
Sankoff, David
author_sort Yu, Zhe
collection PubMed
description We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence.
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spelling pubmed-77755542021-01-02 Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants Yu, Zhe Zheng, Chunfang Albert, Victor A. Sankoff, David Front Genet Genetics We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost—there are few if any relics of the missing sequence. Pseudogenes are rare or extremely transient in this context. The potential exceptions lie exclusively with a few examples of speciation, where the synteny blocks in some larger genomes tolerate degenerate sequence during genomic divergence of two species, but not after whole genome doubling in the same species where fractionation pressure eliminates virtually all non-coding sequence. Frontiers Media S.A. 2020-12-18 /pmc/articles/PMC7775554/ /pubmed/33391353 http://dx.doi.org/10.3389/fgene.2020.603056 Text en Copyright © 2020 Yu, Zheng, Albert and Sankoff. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Yu, Zhe
Zheng, Chunfang
Albert, Victor A.
Sankoff, David
Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants
title Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants
title_full Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants
title_fullStr Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants
title_full_unstemmed Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants
title_short Excision Dominates Pseudogenization During Fractionation After Whole Genome Duplication and in Gene Loss After Speciation in Plants
title_sort excision dominates pseudogenization during fractionation after whole genome duplication and in gene loss after speciation in plants
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775554/
https://www.ncbi.nlm.nih.gov/pubmed/33391353
http://dx.doi.org/10.3389/fgene.2020.603056
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