Evolution of the largest mammalian genome

Autores
Evans, Ben J.; Upham, Nathan S.; Golding, G. Brian; Ojeda, Ricardo Alberto; Ojeda, Agustina Alejandra
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about five million years ago. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrarae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared to the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects ? including during the evolution of hypersaline dietary tolerance in T. barrerae.
Fil: Evans, Ben J.. Mc Master University; Canadá
Fil: Upham, Nathan S.. Mc Master University; Canadá. Field Museum of Natural History; Estados Unidos. University of Yale; Estados Unidos
Fil: Golding, G. Brian. Mc Master University; Canadá
Fil: Ojeda, Ricardo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina
Fil: Ojeda, Agustina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina
Materia
WHOLE GENOME DUPLICATION
REPETITIVE DNA
MAMMALS
RODENTIA
CAVIOMORPHA
OCTODONTIDAE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/43607
Acceder
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Evolution of the largest mammalian genomeEvans, Ben J.Upham, Nathan S.Golding, G. BrianOjeda, Ricardo AlbertoOjeda, Agustina AlejandraWHOLE GENOME DUPLICATIONREPETITIVE DNAMAMMALSRODENTIACAVIOMORPHAOCTODONTIDAEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about five million years ago. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrarae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared to the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects ? including during the evolution of hypersaline dietary tolerance in T. barrerae.Fil: Evans, Ben J.. Mc Master University; CanadáFil: Upham, Nathan S.. Mc Master University; Canadá. Field Museum of Natural History; Estados Unidos. University of Yale; Estados UnidosFil: Golding, G. Brian. Mc Master University; CanadáFil: Ojeda, Ricardo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Ojeda, Agustina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaOxford Academic2017-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/43607Evans, Ben J.; Upham, Nathan S.; Golding, G. Brian; Ojeda, Ricardo Alberto; Ojeda, Agustina Alejandra; Evolution of the largest mammalian genome; Oxford Academic; Genome Biology and Evolution; 9; 6; 6-2017; 1711-17241759-6653CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evx113info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/gbe/article/9/6/1711/3954029info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:36:19Zoai:ri.conicet.gov.ar:11336/43607instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:36:20.048CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Evolution of the largest mammalian genome
title Evolution of the largest mammalian genome
spellingShingle Evolution of the largest mammalian genome
Evans, Ben J.
WHOLE GENOME DUPLICATION
REPETITIVE DNA
MAMMALS
RODENTIA
CAVIOMORPHA
OCTODONTIDAE
title_short Evolution of the largest mammalian genome
title_full Evolution of the largest mammalian genome
title_fullStr Evolution of the largest mammalian genome
title_full_unstemmed Evolution of the largest mammalian genome
title_sort Evolution of the largest mammalian genome
dc.creator.none.fl_str_mv Evans, Ben J.
Upham, Nathan S.
Golding, G. Brian
Ojeda, Ricardo Alberto
Ojeda, Agustina Alejandra
author Evans, Ben J.
author_facet Evans, Ben J.
Upham, Nathan S.
Golding, G. Brian
Ojeda, Ricardo Alberto
Ojeda, Agustina Alejandra
author_role author
author2 Upham, Nathan S.
Golding, G. Brian
Ojeda, Ricardo Alberto
Ojeda, Agustina Alejandra
author2_role author
author
author
author
dc.subject.none.fl_str_mv WHOLE GENOME DUPLICATION
REPETITIVE DNA
MAMMALS
RODENTIA
CAVIOMORPHA
OCTODONTIDAE
topic WHOLE GENOME DUPLICATION
REPETITIVE DNA
MAMMALS
RODENTIA
CAVIOMORPHA
OCTODONTIDAE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about five million years ago. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrarae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared to the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects ? including during the evolution of hypersaline dietary tolerance in T. barrerae.
Fil: Evans, Ben J.. Mc Master University; Canadá
Fil: Upham, Nathan S.. Mc Master University; Canadá. Field Museum of Natural History; Estados Unidos. University of Yale; Estados Unidos
Fil: Golding, G. Brian. Mc Master University; Canadá
Fil: Ojeda, Ricardo Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina
Fil: Ojeda, Agustina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina
description The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about five million years ago. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrarae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared to the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects ? including during the evolution of hypersaline dietary tolerance in T. barrerae.
publishDate 2017
dc.date.none.fl_str_mv 2017-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/43607
Evans, Ben J.; Upham, Nathan S.; Golding, G. Brian; Ojeda, Ricardo Alberto; Ojeda, Agustina Alejandra; Evolution of the largest mammalian genome; Oxford Academic; Genome Biology and Evolution; 9; 6; 6-2017; 1711-1724
1759-6653
CONICET Digital
CONICET
url http://hdl.handle.net/11336/43607
identifier_str_mv Evans, Ben J.; Upham, Nathan S.; Golding, G. Brian; Ojeda, Ricardo Alberto; Ojeda, Agustina Alejandra; Evolution of the largest mammalian genome; Oxford Academic; Genome Biology and Evolution; 9; 6; 6-2017; 1711-1724
1759-6653
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evx113
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/gbe/article/9/6/1711/3954029
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford Academic
publisher.none.fl_str_mv Oxford Academic
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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