Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution

Autores
Trigila, Anabella Paola; Beati, Maria Paula; Montini, Dante; Jovicic, Camila; de la Vega, Paula; Franchini, Lucia Florencia
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The discovery of the genetic mechanisms underlying the emergence of phenotypic novelties is a cornerstone of evolutionary biology. To identify sequences in vertebrate genomes leading to the emergence of clade defining traits, we uncover genomic regions conserved across vertebrates that accumulated substitutions in a faster than neutral rate in the Avian or in the Mammalian basal lineages. We identify 2,888 and 3,476 noncoding avian and mammals accelerated regions, respectively, accumulating in key developmental genes in each lineage. Interestingly, we find that the neuronal transcription factor NPAS3, that carries the largest number of human accelerated regions, also accumulates the largest amount of noncoding mammals accelerated regions. We also detect that four NPAS3 noncoding mammals accelerated regions overlap previously identified human accelerated regions. Thus, we show that noncoding regions of particular large-effect genes are repeatedly targets of accelerated evolution, suggesting the existence of evolutionary hotspots underlying phenotypic innovation in different lineages.
Fil: Trigila, Anabella Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Beati, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Montini, Dante. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Jovicic, Camila. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: de la Vega, Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Franchini, Lucia Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Materia
NPAS3
mammals
birds
noncoding
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/279090
Acceder
id CONICETDig_9043ee4219e2b56f7c89cada3b796424
oai_identifier_str oai:ri.conicet.gov.ar:11336/279090
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolutionTrigila, Anabella PaolaBeati, Maria PaulaMontini, DanteJovicic, Camilade la Vega, PaulaFranchini, Lucia FlorenciaNPAS3mammalsbirdsnoncodinghttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The discovery of the genetic mechanisms underlying the emergence of phenotypic novelties is a cornerstone of evolutionary biology. To identify sequences in vertebrate genomes leading to the emergence of clade defining traits, we uncover genomic regions conserved across vertebrates that accumulated substitutions in a faster than neutral rate in the Avian or in the Mammalian basal lineages. We identify 2,888 and 3,476 noncoding avian and mammals accelerated regions, respectively, accumulating in key developmental genes in each lineage. Interestingly, we find that the neuronal transcription factor NPAS3, that carries the largest number of human accelerated regions, also accumulates the largest amount of noncoding mammals accelerated regions. We also detect that four NPAS3 noncoding mammals accelerated regions overlap previously identified human accelerated regions. Thus, we show that noncoding regions of particular large-effect genes are repeatedly targets of accelerated evolution, suggesting the existence of evolutionary hotspots underlying phenotypic innovation in different lineages.Fil: Trigila, Anabella Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Beati, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Montini, Dante. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Jovicic, Camila. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: de la Vega, Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Franchini, Lucia Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaSpringer2025-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/279090Trigila, Anabella Paola; Beati, Maria Paula; Montini, Dante; Jovicic, Camila; de la Vega, Paula; et al.; Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution; Springer; Nature Communications; 16; 1; 10-2025; 1-192041-1723CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41467-025-64134-2info:eu-repo/semantics/altIdentifier/doi/10.1038/s41467-025-64134-2info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-01-14T11:49:25Zoai:ri.conicet.gov.ar:11336/279090instacron: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:34982026-01-14 11:49:25.893CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
title Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
spellingShingle Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
Trigila, Anabella Paola
NPAS3
mammals
birds
noncoding
title_short Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
title_full Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
title_fullStr Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
title_full_unstemmed Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
title_sort Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution
dc.creator.none.fl_str_mv Trigila, Anabella Paola
Beati, Maria Paula
Montini, Dante
Jovicic, Camila
de la Vega, Paula
Franchini, Lucia Florencia
author Trigila, Anabella Paola
author_facet Trigila, Anabella Paola
Beati, Maria Paula
Montini, Dante
Jovicic, Camila
de la Vega, Paula
Franchini, Lucia Florencia
author_role author
author2 Beati, Maria Paula
Montini, Dante
Jovicic, Camila
de la Vega, Paula
Franchini, Lucia Florencia
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv NPAS3
mammals
birds
noncoding
topic NPAS3
mammals
birds
noncoding
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 discovery of the genetic mechanisms underlying the emergence of phenotypic novelties is a cornerstone of evolutionary biology. To identify sequences in vertebrate genomes leading to the emergence of clade defining traits, we uncover genomic regions conserved across vertebrates that accumulated substitutions in a faster than neutral rate in the Avian or in the Mammalian basal lineages. We identify 2,888 and 3,476 noncoding avian and mammals accelerated regions, respectively, accumulating in key developmental genes in each lineage. Interestingly, we find that the neuronal transcription factor NPAS3, that carries the largest number of human accelerated regions, also accumulates the largest amount of noncoding mammals accelerated regions. We also detect that four NPAS3 noncoding mammals accelerated regions overlap previously identified human accelerated regions. Thus, we show that noncoding regions of particular large-effect genes are repeatedly targets of accelerated evolution, suggesting the existence of evolutionary hotspots underlying phenotypic innovation in different lineages.
Fil: Trigila, Anabella Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Beati, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Montini, Dante. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Jovicic, Camila. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: de la Vega, Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Franchini, Lucia Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
description The discovery of the genetic mechanisms underlying the emergence of phenotypic novelties is a cornerstone of evolutionary biology. To identify sequences in vertebrate genomes leading to the emergence of clade defining traits, we uncover genomic regions conserved across vertebrates that accumulated substitutions in a faster than neutral rate in the Avian or in the Mammalian basal lineages. We identify 2,888 and 3,476 noncoding avian and mammals accelerated regions, respectively, accumulating in key developmental genes in each lineage. Interestingly, we find that the neuronal transcription factor NPAS3, that carries the largest number of human accelerated regions, also accumulates the largest amount of noncoding mammals accelerated regions. We also detect that four NPAS3 noncoding mammals accelerated regions overlap previously identified human accelerated regions. Thus, we show that noncoding regions of particular large-effect genes are repeatedly targets of accelerated evolution, suggesting the existence of evolutionary hotspots underlying phenotypic innovation in different lineages.
publishDate 2025
dc.date.none.fl_str_mv 2025-10
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/11336/279090
Trigila, Anabella Paola; Beati, Maria Paula; Montini, Dante; Jovicic, Camila; de la Vega, Paula; et al.; Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution; Springer; Nature Communications; 16; 1; 10-2025; 1-19
2041-1723
CONICET Digital
CONICET
url http://hdl.handle.net/11336/279090
identifier_str_mv Trigila, Anabella Paola; Beati, Maria Paula; Montini, Dante; Jovicic, Camila; de la Vega, Paula; et al.; Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution; Springer; Nature Communications; 16; 1; 10-2025; 1-19
2041-1723
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41467-025-64134-2
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41467-025-64134-2
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
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
_version_ 1854320968993865728
score 13.113929

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