Evidence for the Transcription of a Satellite DNA Widely Found in Frogs

Autores
Nunes Pompeo, Jennifer; Pretto Gatto, Kaleb; Baldo, Juan Diego; Bolsoni Lourenço, Luciana
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: The satellite DNA (satDNA) PcP190 has been identified in multiple frog species from seven phylogenetically distant families within Hyloidea, indicating its broad distribution. This satDNA consists of repeats of approximately 190 bp and exhibits a highly conserved region (CR) of 120 bp, which is similar to the transcribed region of 5S ribosomal DNA (rDNA), and a hypervariable region (HR) that varies in size and nucleotide composition among and within species. Here, to improve our understanding of PcP190 satDNA, we searched for evidence of its transcription in the available transcriptomes of Rhinella marina (Bufonidae) and Engystomops pustulosus (Leptodactylidae), two phylogenetically distantly related species. Methods: We first characterized the 5S rDNA and PcP190 sequences in these species by searching for them in available genome assemblies. Next, we used the PcP190 (CR and HR) and 5S rDNA sequences of each species as queries to search for these sequences in RNA-seq libraries. Results: We identified two types of 5S rDNA in each analyzed species, with a new type found in E. pustulosus. Our results also revealed a novel type of PcP190 sequence in R. marina and a new subtype of PcP-1 in E. pustulosus. Transcriptome analyses confirmed the expected transcription of the 5S rRNA gene and showed transcription of both the CR and HR of the PcP190 satDNA in both species and in different tissues. Conclusions: As the entire repeat of this satDNA is susceptible to transcription, the high variability observed in the HR cannot be attributed to transcriptional activity confined to the CR.
Fil: Nunes Pompeo, Jennifer. Universidade Estadual de Campinas. Instituto de Biología; Brasil
Fil: Pretto Gatto, Kaleb. Universidade Federal do Paraná; Brasil
Fil: Baldo, Juan Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina
Fil: Bolsoni Lourenço, Luciana. Universidade Estadual de Campinas. Instituto de Biología; Brasil
Materia
Anura
Transcriptome
Bioinformatics
Genomics
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:11336/263151
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/263151
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Evidence for the Transcription of a Satellite DNA Widely Found in FrogsNunes Pompeo, JenniferPretto Gatto, KalebBaldo, Juan DiegoBolsoni Lourenço, LucianaAnuraTranscriptomeBioinformaticsGenomicshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: The satellite DNA (satDNA) PcP190 has been identified in multiple frog species from seven phylogenetically distant families within Hyloidea, indicating its broad distribution. This satDNA consists of repeats of approximately 190 bp and exhibits a highly conserved region (CR) of 120 bp, which is similar to the transcribed region of 5S ribosomal DNA (rDNA), and a hypervariable region (HR) that varies in size and nucleotide composition among and within species. Here, to improve our understanding of PcP190 satDNA, we searched for evidence of its transcription in the available transcriptomes of Rhinella marina (Bufonidae) and Engystomops pustulosus (Leptodactylidae), two phylogenetically distantly related species. Methods: We first characterized the 5S rDNA and PcP190 sequences in these species by searching for them in available genome assemblies. Next, we used the PcP190 (CR and HR) and 5S rDNA sequences of each species as queries to search for these sequences in RNA-seq libraries. Results: We identified two types of 5S rDNA in each analyzed species, with a new type found in E. pustulosus. Our results also revealed a novel type of PcP190 sequence in R. marina and a new subtype of PcP-1 in E. pustulosus. Transcriptome analyses confirmed the expected transcription of the 5S rRNA gene and showed transcription of both the CR and HR of the PcP190 satDNA in both species and in different tissues. Conclusions: As the entire repeat of this satDNA is susceptible to transcription, the high variability observed in the HR cannot be attributed to transcriptional activity confined to the CR.Fil: Nunes Pompeo, Jennifer. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Pretto Gatto, Kaleb. Universidade Federal do Paraná; BrasilFil: Baldo, Juan Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Bolsoni Lourenço, Luciana. Universidade Estadual de Campinas. Instituto de Biología; BrasilMultidisciplinary Digital Publishing Institute2024-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/263151Nunes Pompeo, Jennifer; Pretto Gatto, Kaleb; Baldo, Juan Diego; Bolsoni Lourenço, Luciana; Evidence for the Transcription of a Satellite DNA Widely Found in Frogs; Multidisciplinary Digital Publishing Institute; Genes; 15; 12; 12-2024; 1-152073-4425CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2073-4425/15/12/1572info:eu-repo/semantics/altIdentifier/doi/10.3390/genes15121572info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:02:03Zoai:ri.conicet.gov.ar:11336/263151instacron: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:34982025-09-10 13:02:03.361CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
title Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
spellingShingle Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
Nunes Pompeo, Jennifer
Anura
Transcriptome
Bioinformatics
Genomics
title_short Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
title_full Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
title_fullStr Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
title_full_unstemmed Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
title_sort Evidence for the Transcription of a Satellite DNA Widely Found in Frogs
dc.creator.none.fl_str_mv Nunes Pompeo, Jennifer
Pretto Gatto, Kaleb
Baldo, Juan Diego
Bolsoni Lourenço, Luciana
author Nunes Pompeo, Jennifer
author_facet Nunes Pompeo, Jennifer
Pretto Gatto, Kaleb
Baldo, Juan Diego
Bolsoni Lourenço, Luciana
author_role author
author2 Pretto Gatto, Kaleb
Baldo, Juan Diego
Bolsoni Lourenço, Luciana
author2_role author
author
author
dc.subject.none.fl_str_mv Anura
Transcriptome
Bioinformatics
Genomics
topic Anura
Transcriptome
Bioinformatics
Genomics
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: The satellite DNA (satDNA) PcP190 has been identified in multiple frog species from seven phylogenetically distant families within Hyloidea, indicating its broad distribution. This satDNA consists of repeats of approximately 190 bp and exhibits a highly conserved region (CR) of 120 bp, which is similar to the transcribed region of 5S ribosomal DNA (rDNA), and a hypervariable region (HR) that varies in size and nucleotide composition among and within species. Here, to improve our understanding of PcP190 satDNA, we searched for evidence of its transcription in the available transcriptomes of Rhinella marina (Bufonidae) and Engystomops pustulosus (Leptodactylidae), two phylogenetically distantly related species. Methods: We first characterized the 5S rDNA and PcP190 sequences in these species by searching for them in available genome assemblies. Next, we used the PcP190 (CR and HR) and 5S rDNA sequences of each species as queries to search for these sequences in RNA-seq libraries. Results: We identified two types of 5S rDNA in each analyzed species, with a new type found in E. pustulosus. Our results also revealed a novel type of PcP190 sequence in R. marina and a new subtype of PcP-1 in E. pustulosus. Transcriptome analyses confirmed the expected transcription of the 5S rRNA gene and showed transcription of both the CR and HR of the PcP190 satDNA in both species and in different tissues. Conclusions: As the entire repeat of this satDNA is susceptible to transcription, the high variability observed in the HR cannot be attributed to transcriptional activity confined to the CR.
Fil: Nunes Pompeo, Jennifer. Universidade Estadual de Campinas. Instituto de Biología; Brasil
Fil: Pretto Gatto, Kaleb. Universidade Federal do Paraná; Brasil
Fil: Baldo, Juan Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; Argentina
Fil: Bolsoni Lourenço, Luciana. Universidade Estadual de Campinas. Instituto de Biología; Brasil
description Background: The satellite DNA (satDNA) PcP190 has been identified in multiple frog species from seven phylogenetically distant families within Hyloidea, indicating its broad distribution. This satDNA consists of repeats of approximately 190 bp and exhibits a highly conserved region (CR) of 120 bp, which is similar to the transcribed region of 5S ribosomal DNA (rDNA), and a hypervariable region (HR) that varies in size and nucleotide composition among and within species. Here, to improve our understanding of PcP190 satDNA, we searched for evidence of its transcription in the available transcriptomes of Rhinella marina (Bufonidae) and Engystomops pustulosus (Leptodactylidae), two phylogenetically distantly related species. Methods: We first characterized the 5S rDNA and PcP190 sequences in these species by searching for them in available genome assemblies. Next, we used the PcP190 (CR and HR) and 5S rDNA sequences of each species as queries to search for these sequences in RNA-seq libraries. Results: We identified two types of 5S rDNA in each analyzed species, with a new type found in E. pustulosus. Our results also revealed a novel type of PcP190 sequence in R. marina and a new subtype of PcP-1 in E. pustulosus. Transcriptome analyses confirmed the expected transcription of the 5S rRNA gene and showed transcription of both the CR and HR of the PcP190 satDNA in both species and in different tissues. Conclusions: As the entire repeat of this satDNA is susceptible to transcription, the high variability observed in the HR cannot be attributed to transcriptional activity confined to the CR.
publishDate 2024
dc.date.none.fl_str_mv 2024-12
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/11336/263151
Nunes Pompeo, Jennifer; Pretto Gatto, Kaleb; Baldo, Juan Diego; Bolsoni Lourenço, Luciana; Evidence for the Transcription of a Satellite DNA Widely Found in Frogs; Multidisciplinary Digital Publishing Institute; Genes; 15; 12; 12-2024; 1-15
2073-4425
CONICET Digital
CONICET
url http://hdl.handle.net/11336/263151
identifier_str_mv Nunes Pompeo, Jennifer; Pretto Gatto, Kaleb; Baldo, Juan Diego; Bolsoni Lourenço, Luciana; Evidence for the Transcription of a Satellite DNA Widely Found in Frogs; Multidisciplinary Digital Publishing Institute; Genes; 15; 12; 12-2024; 1-15
2073-4425
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/2073-4425/15/12/1572
info:eu-repo/semantics/altIdentifier/doi/10.3390/genes15121572
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 Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
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 12.993085

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