Dataset.

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/269729
Digital.CSIC. Repositorio Institucional del CSIC
  • Baker, William J.
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigue, Laura
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James
  • Cook, Jeffrey
  • Cowan, Robyn
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego, Berta
  • Johnson, Matthew
  • Kim, Jan
  • Leempoel, Kevin
  • Maurin, Olivier
  • McGinnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman
  • Zuntini, Alexandre
  • Eiserhardt, Wolf
  • Kersey, Paul
  • Leitch, Ilia J.
  • Forest, Félix
Software https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife, The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections., Calleva Foundation. Sackler Trust. Garfield Weston Foundation, Peer reviewed
 
DOI: http://hdl.handle.net/10261/269729
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/269729

HANDLE: http://hdl.handle.net/10261/269729
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/269729
 
Ver en: http://hdl.handle.net/10261/269729
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/269729

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/279677
Artículo científico (article). 2022

A COMPREHENSIVE PHYLOGENOMIC PLATFORM FOR EXPLORING THE ANGIOSPERM TREE OF LIFE

Digital.CSIC. Repositorio Institucional del CSIC
  • Baker, William J.
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigue, Laura
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James
  • Cook, Jeffrey
  • Cowan, Robyn
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego, Berta
  • Johnson, Matthew
  • Kim, Jan
  • Leempoel, Kevin
  • Maurin, Olivier
  • McGinnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman
  • Zuntini, Alexandre
  • Eiserhardt, Wolf
  • Kersey, Paul
  • Leitch, Ilia J.
  • Forest, Félix
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%⁠) and 2333 genera (17%⁠). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.], This work was supported by grants from the Calleva Foundation and the Sackler Trust to the Plant and Fungal Trees of Life project at the Royal Botanic Gardens, Kew. Additional support was received from the Garfield Weston Foundation, as part of the Global Tree Seed Bank Programme., Peer reviewed




Dipòsit Digital de Documents de la UAB
oai:ddd.uab.cat:256111
Artículo científico (article). 2021

A COMPREHENSIVE PHYLOGENOMIC PLATFORM FOR EXPLORING THE ANGIOSPERM TREE OF LIFE

Dipòsit Digital de Documents de la UAB
  • Baker, William J..|||0000-0001-6727-1831
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigué, Laura|||0000-0001-7114-5168
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James J.
  • Cook, Jeffrey
  • Cowan, Robyn S.
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego Páramo, Berta|||0000-0002-2016-7161
  • Johnson, Matthew G.
  • Kim, Jan T.
  • Leempoel, Kevin
  • Maurin, Olivier
  • Mcginnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman J.
  • Zuntini, Alexandre R.
  • Eiserhardt, Wolf L.|||0000-0002-8136-5233
  • Kersey, Paul J.|||0000-0002-7054-800X
  • Leitch, Ilia J.
  • Forest, Félix
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96) and 2333 genera (17). A "first pass" angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world's natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]




Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/269729
Dataset. 2021

A COMPREHENSIVE PHYLOGENOMIC PLATFORM FOR EXPLORING THE ANGIOSPERM TREE OF LIFE

Digital.CSIC. Repositorio Institucional del CSIC
  • Baker, William J.
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigue, Laura
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James
  • Cook, Jeffrey
  • Cowan, Robyn
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego, Berta
  • Johnson, Matthew
  • Kim, Jan
  • Leempoel, Kevin
  • Maurin, Olivier
  • McGinnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman
  • Zuntini, Alexandre
  • Eiserhardt, Wolf
  • Kersey, Paul
  • Leitch, Ilia J.
  • Forest, Félix
Software https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife, The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections., Calleva Foundation. Sackler Trust. Garfield Weston Foundation, Peer reviewed




Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330558
Dataset. 2022

A COMPREHENSIVE PHYLOGENOMIC PLATFORM FOR EXPLORING THE ANGIOSPERM TREE OF LIFE [DATASET]

Digital.CSIC. Repositorio Institucional del CSIC
  • Baker, William J.
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigué, Laura R.
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James
  • Cook, Jeffrey
  • Cowan, Robyn
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego, Berta
  • Johnson, Matthew
  • Kim, Jan
  • Leempoel, Kevin
  • Maurin, Olivier
  • McGinnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman
  • Zuntini, Alexandre
  • Eiserhardt, Wolf
  • Kersey, Paul
  • Leitch, Ilia J.
  • Forest, Félix
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections., Calleva Foundation Sackler Trust Garfield Weston Foundation, Peer reviewed




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