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2024
Journal article
Phylogenomics and the rise of the angiosperms
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on...Zuntini, Alexandre R. ; Carruthers, Tom ; Maurin, Olivier ; Bailey, Paul C. ; Leempoel, Kevin …
Plant evolution, Angiosperms, Phylogenetics, Speciation, and Phylogenomics
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2022
Journal article
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.
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... -
2021
Journal article
Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family.
Siniscalchi, Carolina M. ; Hidalgo, Oriane ; Palazzesi, Luis ; Pellicer, Jaume ; Pokorny, Lisa …
Target capture, Paralogy , Asteraceae , Angiosperms, and Phylogenomics
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2021
Journal article
Settling a family feud: A high-level phylogenomic framework for the gentianales based on 353 nuclear genes and partial plastomes.
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2018
Journal article
A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design.... -
2020
Journal article
Tackling Rapid Radiations With Targeted Sequencing
In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a... -
2019
Journal article
Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms
The world’s herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented...