Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1111/evo.14287 http://hdl.handle.net/11449/221894 |
Resumo: | Multigene families are essential components of eukaryotic genomes and play key roles either structurally and functionally. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in 10 species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and fluorescence in situ hybridization mapping, we find substantial differences between species, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intragenomic analysis of Schistocerca gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies, were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last 8 million years, and the occurrence of intra- and interchromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs in Schistocerca, contributing to the advance of comparative genomics for this important grasshopper genus. |
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Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomesBirth-and-deathconcerted evolutionFISHlarge genomesrepetitive DNAstransposable elementsMultigene families are essential components of eukaryotic genomes and play key roles either structurally and functionally. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in 10 species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and fluorescence in situ hybridization mapping, we find substantial differences between species, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intragenomic analysis of Schistocerca gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies, were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last 8 million years, and the occurrence of intra- and interchromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs in Schistocerca, contributing to the advance of comparative genomics for this important grasshopper genus.National Science FoundationDepartamento de Biologia Geral e Aplicada UNESP – Univ Estadual Paulista Instituto de Biociências/IBDepartment of Entomology Texas A&M UniversityDepartment of Organismal Biology – Systematic Biology Evolutionary Biology Centre Uppsala UniversityPopulation Ecology Group Institute of Ecology and Evolution Friedrich Schiller University JenaDepartamento de Biologia Geral e Aplicada UNESP – Univ Estadual Paulista Instituto de Biociências/IBNational Science Foundation: IOS-1253493Universidade Estadual Paulista (UNESP)Texas A&M UniversityUppsala UniversityFriedrich Schiller University JenaMartí, Emiliano [UNESP]Milani, Diogo [UNESP]Bardella, Vanessa B. [UNESP]Albuquerque, Lucas [UNESP]Song, HojunPalacios-Gimenez, Octavio M.Cabral-de-Mello, Diogo C. [UNESP]2022-04-28T19:41:07Z2022-04-28T19:41:07Z2021-08-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article2027-2041http://dx.doi.org/10.1111/evo.14287Evolution, v. 75, n. 8, p. 2027-2041, 2021.1558-56460014-3820http://hdl.handle.net/11449/22189410.1111/evo.142872-s2.0-85109095887Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengEvolutioninfo:eu-repo/semantics/openAccess2022-04-28T19:41:07Zoai:repositorio.unesp.br:11449/221894Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:11:20.335960Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes |
title |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes |
spellingShingle |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes Martí, Emiliano [UNESP] Birth-and-death concerted evolution FISH large genomes repetitive DNAs transposable elements |
title_short |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes |
title_full |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes |
title_fullStr |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes |
title_full_unstemmed |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes |
title_sort |
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes |
author |
Martí, Emiliano [UNESP] |
author_facet |
Martí, Emiliano [UNESP] Milani, Diogo [UNESP] Bardella, Vanessa B. [UNESP] Albuquerque, Lucas [UNESP] Song, Hojun Palacios-Gimenez, Octavio M. Cabral-de-Mello, Diogo C. [UNESP] |
author_role |
author |
author2 |
Milani, Diogo [UNESP] Bardella, Vanessa B. [UNESP] Albuquerque, Lucas [UNESP] Song, Hojun Palacios-Gimenez, Octavio M. Cabral-de-Mello, Diogo C. [UNESP] |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Texas A&M University Uppsala University Friedrich Schiller University Jena |
dc.contributor.author.fl_str_mv |
Martí, Emiliano [UNESP] Milani, Diogo [UNESP] Bardella, Vanessa B. [UNESP] Albuquerque, Lucas [UNESP] Song, Hojun Palacios-Gimenez, Octavio M. Cabral-de-Mello, Diogo C. [UNESP] |
dc.subject.por.fl_str_mv |
Birth-and-death concerted evolution FISH large genomes repetitive DNAs transposable elements |
topic |
Birth-and-death concerted evolution FISH large genomes repetitive DNAs transposable elements |
description |
Multigene families are essential components of eukaryotic genomes and play key roles either structurally and functionally. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in 10 species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and fluorescence in situ hybridization mapping, we find substantial differences between species, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intragenomic analysis of Schistocerca gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies, were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last 8 million years, and the occurrence of intra- and interchromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs in Schistocerca, contributing to the advance of comparative genomics for this important grasshopper genus. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-08-01 2022-04-28T19:41:07Z 2022-04-28T19:41:07Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1111/evo.14287 Evolution, v. 75, n. 8, p. 2027-2041, 2021. 1558-5646 0014-3820 http://hdl.handle.net/11449/221894 10.1111/evo.14287 2-s2.0-85109095887 |
url |
http://dx.doi.org/10.1111/evo.14287 http://hdl.handle.net/11449/221894 |
identifier_str_mv |
Evolution, v. 75, n. 8, p. 2027-2041, 2021. 1558-5646 0014-3820 10.1111/evo.14287 2-s2.0-85109095887 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Evolution |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
2027-2041 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1808128617054470144 |