Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes

Autores
Magallanes Alba, Melisa Eliana; Baricalla, Agustin Ariel; Feijoo, Matias Pablo; D'elia, Guillermo; Naya, Daniel E.; Lessa, Enrique P.
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Abrothrix olivacea (Waterhouse, 1837), the olive grass mouse, is a widely distributedsigmodontine rodent that inhabits a broad range of environments, from the hyper ariddeserts of southernmost Perú and northern Chile to the Patagonian steppe to the humidtemperate rainforests of southern South America. Its extensive ecological breadth, coupledwith physiological adaptations to water scarcity, makes it an ideal model for studyingenvironmental responses and phenotypic plasticity. Here, we present the first de novoscaffold-level genome assembly of A. olivacea, generated from short-read DNA sequencing.The 2.25 Gb assembly achieved a scaffold N50 of 123 Mb and a BUSCO completenessscore of 98.61%, indicating high sequence completeness. Genome annotation identified21,476 protein-coding genes, providing a valuable resource for evolutionary, ecological, andfunctional genomics. As a case study, we used this reference genome to explore geneexpression and genetic divergence in kidney tissue from individuals inhabiting contrastingenvironments: the southern Andean rainforest and the Patagonian steppe. By integratingsingle-cell transcriptomic data from Mus musculus, we performed cell type deconvolution,revealing environment-specific expression patterns linked to renal function. This newgenomic resource opens avenues for investigating local adaptation, population structure,and conservation genetics in one of South America´s most ecologically versatile and widelydistributed rodents.
Fil: Magallanes Alba, Melisa Eliana. Universidad de la República. Facultad de Ciencias; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Baricalla, Agustin Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; Argentina
Fil: Feijoo, Matias Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de la Republica. Centro Universitario Regional del Este.; Uruguay
Fil: D'elia, Guillermo. Universidad Austral de Chile; Chile
Fil: Naya, Daniel E.. Universidad de la República. Facultad de Ciencias; Uruguay
Fil: Lessa, Enrique P.. Universidad de la República. Facultad de Ciencias; Uruguay
Materia
GENOME ASSEMBLY
KIDNEY
TRANSCRIPTOMIC
COMPARATIVE
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:11336/291128
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/291128
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomesMagallanes Alba, Melisa ElianaBaricalla, Agustin ArielFeijoo, Matias PabloD'elia, GuillermoNaya, Daniel E.Lessa, Enrique P.GENOME ASSEMBLYKIDNEYTRANSCRIPTOMICCOMPARATIVEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Abrothrix olivacea (Waterhouse, 1837), the olive grass mouse, is a widely distributedsigmodontine rodent that inhabits a broad range of environments, from the hyper ariddeserts of southernmost Perú and northern Chile to the Patagonian steppe to the humidtemperate rainforests of southern South America. Its extensive ecological breadth, coupledwith physiological adaptations to water scarcity, makes it an ideal model for studyingenvironmental responses and phenotypic plasticity. Here, we present the first de novoscaffold-level genome assembly of A. olivacea, generated from short-read DNA sequencing.The 2.25 Gb assembly achieved a scaffold N50 of 123 Mb and a BUSCO completenessscore of 98.61%, indicating high sequence completeness. Genome annotation identified21,476 protein-coding genes, providing a valuable resource for evolutionary, ecological, andfunctional genomics. As a case study, we used this reference genome to explore geneexpression and genetic divergence in kidney tissue from individuals inhabiting contrastingenvironments: the southern Andean rainforest and the Patagonian steppe. By integratingsingle-cell transcriptomic data from Mus musculus, we performed cell type deconvolution,revealing environment-specific expression patterns linked to renal function. This newgenomic resource opens avenues for investigating local adaptation, population structure,and conservation genetics in one of South America´s most ecologically versatile and widelydistributed rodents.Fil: Magallanes Alba, Melisa Eliana. Universidad de la República. Facultad de Ciencias; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Baricalla, Agustin Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Feijoo, Matias Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de la Republica. Centro Universitario Regional del Este.; UruguayFil: D'elia, Guillermo. Universidad Austral de Chile; ChileFil: Naya, Daniel E.. Universidad de la República. Facultad de Ciencias; UruguayFil: Lessa, Enrique P.. Universidad de la República. Facultad de Ciencias; UruguayCold Spring Harbor Laboratory Press2025-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/291128Magallanes Alba, Melisa Eliana; Baricalla, Agustin Ariel; Feijoo, Matias Pablo; D'elia, Guillermo; Naya, Daniel E.; et al.; Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes; Cold Spring Harbor Laboratory Press; BioRxiv; 9-2025; 1-202692-8205CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1101/2025.09.12.675871info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/2025.09.12.675871v1info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-08-25T15:30:10Zoai:ri.conicet.gov.ar:11336/291128instacron: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:34982026-08-25 15:30:10.628CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
title Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
spellingShingle Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
Magallanes Alba, Melisa Eliana
GENOME ASSEMBLY
KIDNEY
TRANSCRIPTOMIC
COMPARATIVE
title_short Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
title_full Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
title_fullStr Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
title_full_unstemmed Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
title_sort Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
dc.creator.none.fl_str_mv Magallanes Alba, Melisa Eliana
Baricalla, Agustin Ariel
Feijoo, Matias Pablo
D'elia, Guillermo
Naya, Daniel E.
Lessa, Enrique P.
author Magallanes Alba, Melisa Eliana
author_facet Magallanes Alba, Melisa Eliana
Baricalla, Agustin Ariel
Feijoo, Matias Pablo
D'elia, Guillermo
Naya, Daniel E.
Lessa, Enrique P.
author_role author
author2 Baricalla, Agustin Ariel
Feijoo, Matias Pablo
D'elia, Guillermo
Naya, Daniel E.
Lessa, Enrique P.
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv GENOME ASSEMBLY
KIDNEY
TRANSCRIPTOMIC
COMPARATIVE
topic GENOME ASSEMBLY
KIDNEY
TRANSCRIPTOMIC
COMPARATIVE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Abrothrix olivacea (Waterhouse, 1837), the olive grass mouse, is a widely distributedsigmodontine rodent that inhabits a broad range of environments, from the hyper ariddeserts of southernmost Perú and northern Chile to the Patagonian steppe to the humidtemperate rainforests of southern South America. Its extensive ecological breadth, coupledwith physiological adaptations to water scarcity, makes it an ideal model for studyingenvironmental responses and phenotypic plasticity. Here, we present the first de novoscaffold-level genome assembly of A. olivacea, generated from short-read DNA sequencing.The 2.25 Gb assembly achieved a scaffold N50 of 123 Mb and a BUSCO completenessscore of 98.61%, indicating high sequence completeness. Genome annotation identified21,476 protein-coding genes, providing a valuable resource for evolutionary, ecological, andfunctional genomics. As a case study, we used this reference genome to explore geneexpression and genetic divergence in kidney tissue from individuals inhabiting contrastingenvironments: the southern Andean rainforest and the Patagonian steppe. By integratingsingle-cell transcriptomic data from Mus musculus, we performed cell type deconvolution,revealing environment-specific expression patterns linked to renal function. This newgenomic resource opens avenues for investigating local adaptation, population structure,and conservation genetics in one of South America´s most ecologically versatile and widelydistributed rodents.
Fil: Magallanes Alba, Melisa Eliana. Universidad de la República. Facultad de Ciencias; Uruguay. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Baricalla, Agustin Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; Argentina
Fil: Feijoo, Matias Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de la Republica. Centro Universitario Regional del Este.; Uruguay
Fil: D'elia, Guillermo. Universidad Austral de Chile; Chile
Fil: Naya, Daniel E.. Universidad de la República. Facultad de Ciencias; Uruguay
Fil: Lessa, Enrique P.. Universidad de la República. Facultad de Ciencias; Uruguay
description Abrothrix olivacea (Waterhouse, 1837), the olive grass mouse, is a widely distributedsigmodontine rodent that inhabits a broad range of environments, from the hyper ariddeserts of southernmost Perú and northern Chile to the Patagonian steppe to the humidtemperate rainforests of southern South America. Its extensive ecological breadth, coupledwith physiological adaptations to water scarcity, makes it an ideal model for studyingenvironmental responses and phenotypic plasticity. Here, we present the first de novoscaffold-level genome assembly of A. olivacea, generated from short-read DNA sequencing.The 2.25 Gb assembly achieved a scaffold N50 of 123 Mb and a BUSCO completenessscore of 98.61%, indicating high sequence completeness. Genome annotation identified21,476 protein-coding genes, providing a valuable resource for evolutionary, ecological, andfunctional genomics. As a case study, we used this reference genome to explore geneexpression and genetic divergence in kidney tissue from individuals inhabiting contrastingenvironments: the southern Andean rainforest and the Patagonian steppe. By integratingsingle-cell transcriptomic data from Mus musculus, we performed cell type deconvolution,revealing environment-specific expression patterns linked to renal function. This newgenomic resource opens avenues for investigating local adaptation, population structure,and conservation genetics in one of South America´s most ecologically versatile and widelydistributed rodents.
publishDate 2025
dc.date.none.fl_str_mv 2025-09
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/11336/291128
Magallanes Alba, Melisa Eliana; Baricalla, Agustin Ariel; Feijoo, Matias Pablo; D'elia, Guillermo; Naya, Daniel E.; et al.; Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes; Cold Spring Harbor Laboratory Press; BioRxiv; 9-2025; 1-20
2692-8205
CONICET Digital
CONICET
url http://hdl.handle.net/11336/291128
identifier_str_mv Magallanes Alba, Melisa Eliana; Baricalla, Agustin Ariel; Feijoo, Matias Pablo; D'elia, Guillermo; Naya, Daniel E.; et al.; Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes; Cold Spring Harbor Laboratory Press; BioRxiv; 9-2025; 1-20
2692-8205
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1101/2025.09.12.675871
info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/2025.09.12.675871v1
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 Cold Spring Harbor Laboratory Press
publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
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 13.265058

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