Structural characterization and duplication modes of pseudogenes in plants

Abstract We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all...

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Autores principales: Flavia Mascagni, Gabriele Usai, Andrea Cavallini, Andrea Porceddu
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Publicado: Nature Portfolio 2021
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spelling oai:doaj.org-article:cfbd35d07b36407b8c0287c7dc36632c2021-12-02T11:35:41ZStructural characterization and duplication modes of pseudogenes in plants10.1038/s41598-021-84778-62045-2322https://doaj.org/article/cfbd35d07b36407b8c0287c7dc36632c2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-84778-6https://doaj.org/toc/2045-2322Abstract We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.Flavia MascagniGabriele UsaiAndrea CavalliniAndrea PorcedduNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Flavia Mascagni
Gabriele Usai
Andrea Cavallini
Andrea Porceddu
Structural characterization and duplication modes of pseudogenes in plants
description Abstract We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.
format article
author Flavia Mascagni
Gabriele Usai
Andrea Cavallini
Andrea Porceddu
author_facet Flavia Mascagni
Gabriele Usai
Andrea Cavallini
Andrea Porceddu
author_sort Flavia Mascagni
title Structural characterization and duplication modes of pseudogenes in plants
title_short Structural characterization and duplication modes of pseudogenes in plants
title_full Structural characterization and duplication modes of pseudogenes in plants
title_fullStr Structural characterization and duplication modes of pseudogenes in plants
title_full_unstemmed Structural characterization and duplication modes of pseudogenes in plants
title_sort structural characterization and duplication modes of pseudogenes in plants
publisher Nature Portfolio
publishDate 2021
url https://doaj.org/article/cfbd35d07b36407b8c0287c7dc36632c
work_keys_str_mv AT flaviamascagni structuralcharacterizationandduplicationmodesofpseudogenesinplants
AT gabrieleusai structuralcharacterizationandduplicationmodesofpseudogenesinplants
AT andreacavallini structuralcharacterizationandduplicationmodesofpseudogenesinplants
AT andreaporceddu structuralcharacterizationandduplicationmodesofpseudogenesinplants
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