Angiosperms353

Angiosperms353
Name	Angiosperms353
Type	Genetic marker panel
Scope	Angiosperms
Developed	2019
Developers	Royal Botanic Gardens, Kew; Missouri Botanical Garden; Natural History Museum, London
Applications	Phylogenomics, systematics, conservation genomics

Angiosperms353 Angiosperms353 is a standardized target enrichment probe set for flowering plants developed to enable wide comparative genomic studies across angiosperms. It was devised to facilitate phylogenetic reconstruction, population-level analyses, and integration of datasets across institutions such as the Royal Botanic Gardens, Kew, the Missouri Botanical Garden, the Natural History Museum, London, and collaborators associated with the Global Genome Initiative and the International Barcode of Life project. The panel balances broad taxonomic scope with practical laboratory workflows used by herbaria, botanical gardens, and genomics consortia.

Introduction

The Angiosperms353 initiative emerged from collaborations linking Royal Botanic Gardens, Kew, Missouri Botanical Garden, Natural History Museum, London, Smithsonian Institution, and researchers affiliated with University of Oxford and University of Cambridge to address challenges encountered in projects like the Tree of Life synthesis and the Angiosperm Phylogeny Group updates. It responds to prior efforts including probe panels from Humboldt-Universität zu Berlin groups and methodological advances exemplified by studies at Harvard University, Yale University, and University of California, Berkeley. Funders and stakeholders have included the National Science Foundation (United States), Newton Fund, and biodiversity initiatives coordinated with the Royal Society and the Wellcome Trust.

Marker panel design and loci composition

Angiosperms353 comprises 353 nuclear loci selected for single- or low-copy representation and phylogenetic informativeness across major clades of Angiosperms. The design draws on transcriptomes and genomes produced by teams at Joint Genome Institute, Salk Institute, Max Planck Society, and databases curated by GenBank and the European Nucleotide Archive. Loci selection referenced genomic resources from model and non-model taxa including datasets from Arabidopsis thaliana studies at European Molecular Biology Laboratory and comparative genomics from University of Chicago and Cornell University. Probe tiling and sequence divergence considerations were informed by methods developed at Broad Institute and empirical tests published by groups at University of Florida and University of Wisconsin–Madison.

Applications in phylogenomics and systematics

Researchers apply Angiosperms353 in broad-scale phylogenetic reconstructions connecting to long-standing syntheses by the Angiosperm Phylogeny Group and regional floristic projects led by institutions like Botanic Gardens Conservation International and the Missouri Botanical Garden herbarium. Case studies include phylogenies integrating data from fieldwork associated with the Royal Botanic Gardens, Kew and population-level analyses in conservation contexts supported by IUCN Red List assessments and restoration programs funded by the World Wildlife Fund. The marker set has been used alongside datasets from projects at Kew Science and the Natural History Museum, London to resolve relationships within families treated in floras such as the Flora of China and the Flora of North America.

Laboratory methods and bioinformatics pipelines

Laboratory protocols for Angiosperms353 employ target enrichment workflows using hybridization capture chemistries produced by providers that collaborate with institutions like Illumina, Inc., Thermo Fisher Scientific, and service labs affiliated with the Wellcome Sanger Institute. Laboratory adaptations have been reported by herbaria including Royal Botanic Gardens, Kew and the New York Botanical Garden for degraded DNA from historical specimens. Bioinformatics pipelines integrating assembly and orthology assessment reference tools and standards developed at Broad Institute and computational groups at University of California, San Diego and Max Planck Institute for Evolutionary Biology; workflows often run on infrastructure provided by XSEDE or cloud services from Amazon Web Services and Google Cloud Platform.

Performance, validation, and limitations

Validation studies led by teams at Missouri Botanical Garden, Royal Botanic Gardens, Kew, and universities such as University of British Columbia and University of Michigan evaluated recovery efficiency, paralogy, and locus dropout across lineages represented in genomic repositories like GenBank. The probe set generally yields high locus recovery across deep and shallow divergences but shows reduced performance in lineages with genome duplications documented in studies from Max Planck Society collaborators and in groups with highly degraded herbarium DNA discussed in reports from the Natural History Museum, London. Limitations include potential bias for taxa underrepresented in original design datasets and challenges with paralog resolution that have motivated complementary approaches used by research groups at Harvard University and Yale University.

Community adoption and datasets

Angiosperms353 has been adopted by consortia including the Global Genome Initiative, regional floristic programs at Royal Botanic Gardens, Kew and the Missouri Botanical Garden, and collaborative networks involving the Smithsonian Institution and Australian National Herbarium. Large aggregated datasets have been deposited in public repositories managed by GenBank and the European Nucleotide Archive and integrated into biodiversity informatics platforms like GBIF and synthesis projects coordinated with the Angiosperm Phylogeny Group and the Tree of Life Web Project. Community resources include shared probe sets distributed through commercial providers and protocol repositories maintained by participating institutions such as Kew Science.

Intellectual property, data sharing, and standards

The Angiosperms353 project emphasizes open science practices consistent with policies of funders like the National Science Foundation (United States), the Wellcome Trust, and initiatives such as the Global Biodiversity Information Facility. Probe designs and sequence datasets are broadly shared via archives including GenBank and standards promoted by organizations like TDWG and the Consortium for the Barcode of Life to facilitate interoperability with floristic and genomic databases curated by institutions such as Royal Botanic Gardens, Kew and the Missouri Botanical Garden. Debates about commercialization of probe manufacturing touch institutions including Illumina, Inc. and legal frameworks influenced by national rules and agreements negotiated through bodies such as the Convention on Biological Diversity and the Nagoya Protocol.

Category:Genomics