Dataset.

Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales) [dataset]

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/369427
Digital.CSIC. Repositorio Institucional del CSIC
  • Pokorny, Lisa
  • Pellicer, Jaume
  • Woudstra, Yannick
  • Christenhusz, Maarten J. M.
  • Garnatje, Teresa
  • Palazzesi, Luis
  • Johnson, Matthew G.
  • Maurin, Olivier
  • Françoso, Elaine
  • Roy, Shyamali
  • Leitch, Ilia J.
  • Forest, Félix
  • Baker, William J.
  • Hidalgo, Oriane
Nuclear and plastid datasets and phylogenomic workflow associated to "Genomic Incongruence Accompanies the Evolution of Flower Symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales)", published in Frontiers in Plant Science 15:1340056. This compressed file (poppy_repo.zip) contains a markdown readme file (poppy_readme.md) describing the phylogenomic workflow followed, as well as two dataset folders (poppy_nuc and poppy_pl) divided into four (aln_nuc, gtr_nuc, sptr_nuc, and chrono_nuc) and three (aln_pl, sptr_pl, and chrono_pl) subfolders, respectively. The nuclear folder (poppy_nuc) comprises shrunk and trimmed alignments (aln_nuc), ML gene trees (gtr_nuc), coalescent species trees (sptr_nuc), and a time tree (chrono_nuc). The plastid folder (poppy_pl) comprises shrunk and trimmed alignments (aln_pl), a concatenated ML species tree (sptr_pl), and a time tree (chrono_pl). The research article is available at https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1340056 (doi: 10.3389/fpls.2024.1340056)., [EN] Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in flower symmetry within the family Papaveraceae. This family presents an astonishing array of floral diversity, with actinomorphic, disymmetric (two perpendicular symmetry axes), and zygomorphic flowers. We generated nuclear and plastid datasets using the Angiosperms353 universal probe set for target capture sequencing (of 353 single-copy nuclear ortholog genes), together with publicly available transcriptome and plastome data mined from open-access online repositories. We relied on the fossil record of the order Ranunculales to date our phylogenies and to establish a timeline of events. Our phylogenomic workflow shows that nuclear-plastid incongruence accompanies topological uncertainties in Ranunculales. A cocktail of incomplete lineage sorting, post-hybridization introgression, and extinction following rapid speciation most likely explain the observed knots in the topology. These knots coincide with major floral symmetry transitions and thus obscure the order of evolutionary events., Plant and Fungal Trees of Life (PAFTOL) N/A Calleva Foundation, Ajut a Grups de Recerca Consolidats (GReB) 2021SGR00315 Government of Catalonia, Ayudas para contratos Ramón y Cajal (Lisa Pokorny) RYC2021-034942-I Ministerio de Ciencia e Innovación, Ayudas para contratos Ramón y Cajal (Jaume Pellicer) RYC-2017-2274 Ministerio de Ciencia e Innovación, H2020 MSCA-ITN-ETN Plant.ID (Yannick Woudstra) 765000 European Union, Peer reviewed
 

DOI: http://hdl.handle.net/10261/369427
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/369427

HANDLE: http://hdl.handle.net/10261/369427
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/369427
 
Ver en: http://hdl.handle.net/10261/369427
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/369427

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/368387
Artículo científico (article). 2024

GENOMIC INCONGRUENCE ACCOMPANIES THE EVOLUTION OF FLOWER SYMMETRY IN EUDICOTS: A CASE STUDY IN THE POPPY FAMILY (PAPAVERACEAE, RANUNCULALES)

Digital.CSIC. Repositorio Institucional del CSIC
  • Pokorny, Lisa
  • Pellicer Moscardó, Jaume
  • Woudstra, Yannick
  • Christenhusz, Maarten J. M.
  • Garnatje, Teresa
  • Palazzesi, Luis
  • Johnson, Matthew G.
  • Maurin, Olivier
  • Roy, Shyamali
  • Leitch, Ilia J.
  • Forest, Félix
  • Baker, William J.
  • Hidalgo, Oriane
Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in flower symmetry within the family Papaveraceae. This family presents an astonishing array of floral diversity, with actinomorphic, disymmetric (two perpendicular symmetry axes), and zygomorphic flowers. We generated nuclear and plastid datasets using the Angiosperms353 universal probe set for target capture sequencing (of 353 single-copy nuclear ortholog genes), together with publicly available transcriptome and plastome data mined from open-access online repositories. We relied on the fossil record of the order Ranunculales to date our phylogenies and to establish a timeline of events. Our phylogenomic workflow shows that nuclear-plastid incongruence accompanies topological uncertainties in Ranunculales. A cocktail of incomplete lineage sorting, post-hybridization introgression, and extinction following rapid speciation most likely explain the observed knots in the topology. These knots coincide with major floral symmetry transitions and thus obscure the order of evolutionary events., The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was supported by grants from the Calleva Foundation to the Plant and Fungal Trees of Life (PAFTOL) research programme at the Royal Botanic Gardens, Kew and the Ajut a Grups de Recerca Consolidats (2021SGR00315) from the Government of Catalonia. LPo benefited from a Ramón y Cajal grant (Ref.: RYC2021-034942-I) funded by MCIN/AEI/10.13039/501100011033 and by the European Union “NextGenerationEU”/PRTR. JP benefited from a Ramón y Cajal grant (Ref.: RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future”. YW benefitted from an Early Career Researcher PhD fellowship, within the H2020 MSCA-ITN-ETN Plant.ID, funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 765000., Peer reviewed




Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/371010
Publicaciones de conferencias: comunicaciones, ponencias, pósters, etc (conferenceObject). 2024

GENOMIC INCONGRUENCE ACCOMPANIES THE EVOLUTION OF FLOWER SYMMETRY IN EUDICOTS: A CASE STUDY IN THE POPPY FAMILY (PAPAVERACEAE)

Digital.CSIC. Repositorio Institucional del CSIC
  • Pokorny, Lisa
  • Pellicer, Jaume
  • Woudstra, Yannick
  • Christenhusz, Maarten J. M.
  • Garnatje, Teresa
  • Palazzesi, Luis
  • Johnson, Matthew G.
  • Maurin, Olivier
  • Françoso, Elaine
  • Roy, Shyamali
  • Leitch, Ilia J.
  • Forest, Félix
  • Baker, William J.
  • Hidalgo, Oriane
Comunicación oral presentada en el XX International Botanical Congress Madrid 21-27 julio 2024




Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/369427
Dataset. 2024

GENOMIC INCONGRUENCE ACCOMPANIES THE EVOLUTION OF FLOWER SYMMETRY IN EUDICOTS: A CASE STUDY IN THE POPPY FAMILY (PAPAVERACEAE, RANUNCULALES) [DATASET]

Digital.CSIC. Repositorio Institucional del CSIC
  • Pokorny, Lisa
  • Pellicer, Jaume
  • Woudstra, Yannick
  • Christenhusz, Maarten J. M.
  • Garnatje, Teresa
  • Palazzesi, Luis
  • Johnson, Matthew G.
  • Maurin, Olivier
  • Françoso, Elaine
  • Roy, Shyamali
  • Leitch, Ilia J.
  • Forest, Félix
  • Baker, William J.
  • Hidalgo, Oriane
Nuclear and plastid datasets and phylogenomic workflow associated to "Genomic Incongruence Accompanies the Evolution of Flower Symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales)", published in Frontiers in Plant Science 15:1340056. This compressed file (poppy_repo.zip) contains a markdown readme file (poppy_readme.md) describing the phylogenomic workflow followed, as well as two dataset folders (poppy_nuc and poppy_pl) divided into four (aln_nuc, gtr_nuc, sptr_nuc, and chrono_nuc) and three (aln_pl, sptr_pl, and chrono_pl) subfolders, respectively. The nuclear folder (poppy_nuc) comprises shrunk and trimmed alignments (aln_nuc), ML gene trees (gtr_nuc), coalescent species trees (sptr_nuc), and a time tree (chrono_nuc). The plastid folder (poppy_pl) comprises shrunk and trimmed alignments (aln_pl), a concatenated ML species tree (sptr_pl), and a time tree (chrono_pl). The research article is available at https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1340056 (doi: 10.3389/fpls.2024.1340056)., [EN] Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in flower symmetry within the family Papaveraceae. This family presents an astonishing array of floral diversity, with actinomorphic, disymmetric (two perpendicular symmetry axes), and zygomorphic flowers. We generated nuclear and plastid datasets using the Angiosperms353 universal probe set for target capture sequencing (of 353 single-copy nuclear ortholog genes), together with publicly available transcriptome and plastome data mined from open-access online repositories. We relied on the fossil record of the order Ranunculales to date our phylogenies and to establish a timeline of events. Our phylogenomic workflow shows that nuclear-plastid incongruence accompanies topological uncertainties in Ranunculales. A cocktail of incomplete lineage sorting, post-hybridization introgression, and extinction following rapid speciation most likely explain the observed knots in the topology. These knots coincide with major floral symmetry transitions and thus obscure the order of evolutionary events., Plant and Fungal Trees of Life (PAFTOL) N/A Calleva Foundation, Ajut a Grups de Recerca Consolidats (GReB) 2021SGR00315 Government of Catalonia, Ayudas para contratos Ramón y Cajal (Lisa Pokorny) RYC2021-034942-I Ministerio de Ciencia e Innovación, Ayudas para contratos Ramón y Cajal (Jaume Pellicer) RYC-2017-2274 Ministerio de Ciencia e Innovación, H2020 MSCA-ITN-ETN Plant.ID (Yannick Woudstra) 765000 European Union, Peer reviewed




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