Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)

Autores
Estêvão, João; Blanco Hortas, Andrés; Rubiolo, Juan Andrés; Aramburu, Óscar; Fernández, Carlos; Gómez Tato, Antonio; Power, Deborah M.; Martínez, Paulino
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Turbot and brill are two congeneric commercial flatfish species with striking differences in skin organization. The calcified appendages in turbot skin are conical tubercles, while in brill, they are elasmoid scales. A skin injury involving epidermal and dermal levels was evaluated 72 h post-injury to compare the skin regeneration processes between both species. An immune-enriched 4x44k turbot oligo-microarray was used to characterize the skin transcriptome and gene expression profiles in both species. RNA-seq was also performed on the brill samples to improve transcriptome characterization and validate the microarray results. A total of 15,854 and 12,447 expressed genes were identified, respectively, in the turbot and brill skin (10,101 shared) using the oligo-microarray (11,953 and 9629 annotated). RNA-seq enabled the identification of 11,838 genes in brill skin (11,339 annotated). Functional annotation of skin transcriptomes was similar in both species, but in turbot, it was enriched on mechanisms related to maintenance of epithelial structure, mannosidase activity, phospholipid binding, and cell membranes, while in brill, it was enriched on biological and gene regulation mechanisms, tissue development, and transferase and catalytic activities. The number of DEGs identified after skin damage in brill and turbot was 439 and 143, respectively (only 14 shared). Functions related to catabolic and metabolic processes, visual and sensorial perception, response to wounding, and wound healing were enriched in turbot DEGs, while metabolism, immune response, oxidative stress, phospholipid binding, and response to stimulus were enriched in brill. The results indicate that differences may be related to the stage of wound repair due to their different skin architecture. This work provides a foundation for future studies directed at skin defense mechanisms, with practical implications in flatfish aquaculture.
Fil: Estêvão, João. Universidad de Porto; Portugal
Fil: Blanco Hortas, Andrés. Universidad de Santiago de Compostela; España
Fil: Rubiolo, Juan Andrés. Universidad Nacional de Rosario. Facultad de Cs.bioquimicas y Farmaceuticas. Laboratorio de Biotecnología Acuática.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina
Fil: Aramburu, Óscar. Universidad de Santiago de Compostela; España
Fil: Fernández, Carlos. Universidad de Santiago de Compostela; España
Fil: Gómez Tato, Antonio. Universidad de Santiago de Compostela; España
Fil: Power, Deborah M.. Universidade do Algarve; Portugal
Fil: Martínez, Paulino. Universidad de Santiago de Compostela; España
Materia
fish skin transcriptome
Scophthalmus maximus
Scophthalmus rhombus
oligo-microarray
RNA-seq
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/272310
Acceder
id CONICETDig_b7349e4287f1fdf816b2069081e4c701
oai_identifier_str oai:ri.conicet.gov.ar:11336/272310
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)Estêvão, JoãoBlanco Hortas, AndrésRubiolo, Juan AndrésAramburu, ÓscarFernández, CarlosGómez Tato, AntonioPower, Deborah M.Martínez, Paulinofish skin transcriptomeScophthalmus maximusScophthalmus rhombusoligo-microarrayRNA-seqhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Turbot and brill are two congeneric commercial flatfish species with striking differences in skin organization. The calcified appendages in turbot skin are conical tubercles, while in brill, they are elasmoid scales. A skin injury involving epidermal and dermal levels was evaluated 72 h post-injury to compare the skin regeneration processes between both species. An immune-enriched 4x44k turbot oligo-microarray was used to characterize the skin transcriptome and gene expression profiles in both species. RNA-seq was also performed on the brill samples to improve transcriptome characterization and validate the microarray results. A total of 15,854 and 12,447 expressed genes were identified, respectively, in the turbot and brill skin (10,101 shared) using the oligo-microarray (11,953 and 9629 annotated). RNA-seq enabled the identification of 11,838 genes in brill skin (11,339 annotated). Functional annotation of skin transcriptomes was similar in both species, but in turbot, it was enriched on mechanisms related to maintenance of epithelial structure, mannosidase activity, phospholipid binding, and cell membranes, while in brill, it was enriched on biological and gene regulation mechanisms, tissue development, and transferase and catalytic activities. The number of DEGs identified after skin damage in brill and turbot was 439 and 143, respectively (only 14 shared). Functions related to catabolic and metabolic processes, visual and sensorial perception, response to wounding, and wound healing were enriched in turbot DEGs, while metabolism, immune response, oxidative stress, phospholipid binding, and response to stimulus were enriched in brill. The results indicate that differences may be related to the stage of wound repair due to their different skin architecture. This work provides a foundation for future studies directed at skin defense mechanisms, with practical implications in flatfish aquaculture.Fil: Estêvão, João. Universidad de Porto; PortugalFil: Blanco Hortas, Andrés. Universidad de Santiago de Compostela; EspañaFil: Rubiolo, Juan Andrés. Universidad Nacional de Rosario. Facultad de Cs.bioquimicas y Farmaceuticas. Laboratorio de Biotecnología Acuática.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; ArgentinaFil: Aramburu, Óscar. Universidad de Santiago de Compostela; EspañaFil: Fernández, Carlos. Universidad de Santiago de Compostela; EspañaFil: Gómez Tato, Antonio. Universidad de Santiago de Compostela; EspañaFil: Power, Deborah M.. Universidade do Algarve; PortugalFil: Martínez, Paulino. Universidad de Santiago de Compostela; EspañaMDPI2024-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/272310Estêvão, João; Blanco Hortas, Andrés; Rubiolo, Juan Andrés; Aramburu, Óscar; Fernández, Carlos; et al.; Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus); MDPI; Fishes; 9; 11; 11-2024; 1-212410-3888CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2410-3888/9/11/462info:eu-repo/semantics/altIdentifier/doi/10.3390/fishes9110462info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:06:38Zoai:ri.conicet.gov.ar:11336/272310instacron: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:34982025-10-22 11:06:38.645CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
title Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
spellingShingle Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
Estêvão, João
fish skin transcriptome
Scophthalmus maximus
Scophthalmus rhombus
oligo-microarray
RNA-seq
title_short Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
title_full Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
title_fullStr Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
title_full_unstemmed Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
title_sort Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus)
dc.creator.none.fl_str_mv Estêvão, João
Blanco Hortas, Andrés
Rubiolo, Juan Andrés
Aramburu, Óscar
Fernández, Carlos
Gómez Tato, Antonio
Power, Deborah M.
Martínez, Paulino
author Estêvão, João
author_facet Estêvão, João
Blanco Hortas, Andrés
Rubiolo, Juan Andrés
Aramburu, Óscar
Fernández, Carlos
Gómez Tato, Antonio
Power, Deborah M.
Martínez, Paulino
author_role author
author2 Blanco Hortas, Andrés
Rubiolo, Juan Andrés
Aramburu, Óscar
Fernández, Carlos
Gómez Tato, Antonio
Power, Deborah M.
Martínez, Paulino
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv fish skin transcriptome
Scophthalmus maximus
Scophthalmus rhombus
oligo-microarray
RNA-seq
topic fish skin transcriptome
Scophthalmus maximus
Scophthalmus rhombus
oligo-microarray
RNA-seq
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Turbot and brill are two congeneric commercial flatfish species with striking differences in skin organization. The calcified appendages in turbot skin are conical tubercles, while in brill, they are elasmoid scales. A skin injury involving epidermal and dermal levels was evaluated 72 h post-injury to compare the skin regeneration processes between both species. An immune-enriched 4x44k turbot oligo-microarray was used to characterize the skin transcriptome and gene expression profiles in both species. RNA-seq was also performed on the brill samples to improve transcriptome characterization and validate the microarray results. A total of 15,854 and 12,447 expressed genes were identified, respectively, in the turbot and brill skin (10,101 shared) using the oligo-microarray (11,953 and 9629 annotated). RNA-seq enabled the identification of 11,838 genes in brill skin (11,339 annotated). Functional annotation of skin transcriptomes was similar in both species, but in turbot, it was enriched on mechanisms related to maintenance of epithelial structure, mannosidase activity, phospholipid binding, and cell membranes, while in brill, it was enriched on biological and gene regulation mechanisms, tissue development, and transferase and catalytic activities. The number of DEGs identified after skin damage in brill and turbot was 439 and 143, respectively (only 14 shared). Functions related to catabolic and metabolic processes, visual and sensorial perception, response to wounding, and wound healing were enriched in turbot DEGs, while metabolism, immune response, oxidative stress, phospholipid binding, and response to stimulus were enriched in brill. The results indicate that differences may be related to the stage of wound repair due to their different skin architecture. This work provides a foundation for future studies directed at skin defense mechanisms, with practical implications in flatfish aquaculture.
Fil: Estêvão, João. Universidad de Porto; Portugal
Fil: Blanco Hortas, Andrés. Universidad de Santiago de Compostela; España
Fil: Rubiolo, Juan Andrés. Universidad Nacional de Rosario. Facultad de Cs.bioquimicas y Farmaceuticas. Laboratorio de Biotecnología Acuática.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentina
Fil: Aramburu, Óscar. Universidad de Santiago de Compostela; España
Fil: Fernández, Carlos. Universidad de Santiago de Compostela; España
Fil: Gómez Tato, Antonio. Universidad de Santiago de Compostela; España
Fil: Power, Deborah M.. Universidade do Algarve; Portugal
Fil: Martínez, Paulino. Universidad de Santiago de Compostela; España
description Turbot and brill are two congeneric commercial flatfish species with striking differences in skin organization. The calcified appendages in turbot skin are conical tubercles, while in brill, they are elasmoid scales. A skin injury involving epidermal and dermal levels was evaluated 72 h post-injury to compare the skin regeneration processes between both species. An immune-enriched 4x44k turbot oligo-microarray was used to characterize the skin transcriptome and gene expression profiles in both species. RNA-seq was also performed on the brill samples to improve transcriptome characterization and validate the microarray results. A total of 15,854 and 12,447 expressed genes were identified, respectively, in the turbot and brill skin (10,101 shared) using the oligo-microarray (11,953 and 9629 annotated). RNA-seq enabled the identification of 11,838 genes in brill skin (11,339 annotated). Functional annotation of skin transcriptomes was similar in both species, but in turbot, it was enriched on mechanisms related to maintenance of epithelial structure, mannosidase activity, phospholipid binding, and cell membranes, while in brill, it was enriched on biological and gene regulation mechanisms, tissue development, and transferase and catalytic activities. The number of DEGs identified after skin damage in brill and turbot was 439 and 143, respectively (only 14 shared). Functions related to catabolic and metabolic processes, visual and sensorial perception, response to wounding, and wound healing were enriched in turbot DEGs, while metabolism, immune response, oxidative stress, phospholipid binding, and response to stimulus were enriched in brill. The results indicate that differences may be related to the stage of wound repair due to their different skin architecture. This work provides a foundation for future studies directed at skin defense mechanisms, with practical implications in flatfish aquaculture.
publishDate 2024
dc.date.none.fl_str_mv 2024-11
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/11336/272310
Estêvão, João; Blanco Hortas, Andrés; Rubiolo, Juan Andrés; Aramburu, Óscar; Fernández, Carlos; et al.; Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus); MDPI; Fishes; 9; 11; 11-2024; 1-21
2410-3888
CONICET Digital
CONICET
url http://hdl.handle.net/11336/272310
identifier_str_mv Estêvão, João; Blanco Hortas, Andrés; Rubiolo, Juan Andrés; Aramburu, Óscar; Fernández, Carlos; et al.; Gene Expression Comparison Between the Injured Tubercule Skin of Turbot (Scophthalmus maximus) and the Scale Skin of Brill (Scophthalmus rhombus); MDPI; Fishes; 9; 11; 11-2024; 1-21
2410-3888
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.mdpi.com/2410-3888/9/11/462
info:eu-repo/semantics/altIdentifier/doi/10.3390/fishes9110462
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
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 12.982451

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