Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module

Autores
Flores Sandoval, Eduardo; Romani, Facundo Alihuen; Bowman, John L.
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 may antagonize the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.
Fil: Flores Sandoval, Eduardo. Monash University; Australia
Fil: Romani, Facundo Alihuen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
Fil: Bowman, John L.. Monash University; Australia
Materia
AUXIN
AUXIN RESPONSE FACTORS
CLASS C ARFS
CO-EXPRESSION
MARCHANTIA
MIR160
REPRODUCTIVE TRANSITIONS
TRANSCRIPTOME
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:11336/86629
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/86629
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory moduleFlores Sandoval, EduardoRomani, Facundo AlihuenBowman, John L.AUXINAUXIN RESPONSE FACTORSCLASS C ARFSCO-EXPRESSIONMARCHANTIAMIR160REPRODUCTIVE TRANSITIONSTRANSCRIPTOMEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 may antagonize the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.Fil: Flores Sandoval, Eduardo. Monash University; AustraliaFil: Romani, Facundo Alihuen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Bowman, John L.. Monash University; AustraliaFrontiers Media S.A.2018-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/86629Flores Sandoval, Eduardo; Romani, Facundo Alihuen; Bowman, John L.; Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module; Frontiers Media S.A.; Frontiers in Plant Science; 9; 10-2018; 1-211664-462XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.3389/fpls.2018.01345info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:56:47Zoai:ri.conicet.gov.ar:11336/86629instacron: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 09:56:48.241CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
title Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
spellingShingle Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
Flores Sandoval, Eduardo
AUXIN
AUXIN RESPONSE FACTORS
CLASS C ARFS
CO-EXPRESSION
MARCHANTIA
MIR160
REPRODUCTIVE TRANSITIONS
TRANSCRIPTOME
title_short Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
title_full Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
title_fullStr Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
title_full_unstemmed Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
title_sort Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module
dc.creator.none.fl_str_mv Flores Sandoval, Eduardo
Romani, Facundo Alihuen
Bowman, John L.
author Flores Sandoval, Eduardo
author_facet Flores Sandoval, Eduardo
Romani, Facundo Alihuen
Bowman, John L.
author_role author
author2 Romani, Facundo Alihuen
Bowman, John L.
author2_role author
author
dc.subject.none.fl_str_mv AUXIN
AUXIN RESPONSE FACTORS
CLASS C ARFS
CO-EXPRESSION
MARCHANTIA
MIR160
REPRODUCTIVE TRANSITIONS
TRANSCRIPTOME
topic AUXIN
AUXIN RESPONSE FACTORS
CLASS C ARFS
CO-EXPRESSION
MARCHANTIA
MIR160
REPRODUCTIVE TRANSITIONS
TRANSCRIPTOME
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 may antagonize the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.
Fil: Flores Sandoval, Eduardo. Monash University; Australia
Fil: Romani, Facundo Alihuen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
Fil: Bowman, John L.. Monash University; Australia
description We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 may antagonize the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.
publishDate 2018
dc.date.none.fl_str_mv 2018-10
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/11336/86629
Flores Sandoval, Eduardo; Romani, Facundo Alihuen; Bowman, John L.; Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module; Frontiers Media S.A.; Frontiers in Plant Science; 9; 10-2018; 1-21
1664-462X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/86629
identifier_str_mv Flores Sandoval, Eduardo; Romani, Facundo Alihuen; Bowman, John L.; Co-expression and transcriptome analysis of marchantia polymorpha transcription factors supports class c arfs as independent actors of an ancient auxin regulatory module; Frontiers Media S.A.; Frontiers in Plant Science; 9; 10-2018; 1-21
1664-462X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.3389/fpls.2018.01345
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 Frontiers Media S.A.
publisher.none.fl_str_mv Frontiers Media S.A.
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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