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Journal article
Giant Fern Genomes Show Complex Evolution Patterns: A Comparative Analysis in Two Species of Tmesipteris (Psilotaceae).
Giant genomes are rare across the plant kingdom and their study has focused almost exclusively on angiosperms and gymnosperms. The scarce genetic data that are available for ferns, however, indicate differences in their genome organization and a lower dynamism compared to other plant groups. Tmesipteris is a small genus of... -
Journal article
Asteraceae as a model system for evolutionary studies: from fossils to genomes.
With c. 24 700 species (10% of all flowering plants), Asteraceae are one of the largest and most phenotypically diverse angiosperm families, with considerable economic and ecological importance. Asteraceae are distributed worldwide, from nearly polar latitudes all the way to the tropics, and occur across a diverse range of habitats...Palazzesi, Luis ; Pellicer, Jaume ; Barreda, Viviana D ; Loeuille, Benoît ; Mandel, Jennifer R …
Phylogenomics, Fossil record, Biogeography, Asteraceae, Evolution, Compositae, and Genome size
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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... -
Journal article
Taming the beast: a revised classification of Cortinariaceae based on genomic data.
Family currently includes only one genus, , which is the largest genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus contains a lot of morphological variation, and its complexity has led many taxonomists...Liimatainen, Kare ; Kim, Jan T. ; Pokorny, Lisa ; Kirk, Paul M. ; Dentinger, Bryn …
HybPiper, Fungariomics, Fungi, Whole genome sequencing, Agaricales, and Museomics
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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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Journal article
A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae
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Journal article
Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set.
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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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Journal article
Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.
Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus... -
Journal article
Resolving generic limits in Cyperaceae tribe Abildgaardieae using targeted sequencing
Morphological characterizations of genera in Cyperaceae tribe Abildgaardieae have been highly problematic and the subject of much debate. Earlier molecular phylogenetic studies based on Sanger sequencing and a limited sampling have indicated that several generic circumscriptions are not monophyletic. Here, we provide the first phylogenetic hypothesis for Abildgaardieae using targeted...Larridon, Isabel ; Zuntini, Alexandre R. ; Barrett, Russell L. ; Wilson, Karen L. ; Bruhl, Jeremy J. …
Fimbristylis, C4 photosynthesis, generic circumscription, Bulbostylis, and Angiosperms353
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Journal article
Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants
The reduced cost of high‐throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per‐sample cost, which... -
Journal article
Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics
Shee, Zhi Qiang ; Frodin, David G. ; Cámara-Leret, Rodrigo ; Pokorny, Lisa
Schefflera, Sequence capture, Historical biogeography, Araliaceae, Target enrichment, Papuasia, New Guinea, and Herbariomics
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Journal article
A roadmap for global synthesis of the plant tree of life
Providing science and society with an integrated, up‐to‐date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience... -
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.... -
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... -
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... -
Journal article
A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)
Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related...Soto Gomez, Marybel ; Pokorny, Lisa ; Kantar, Michael ; Forest, Félix ; Leitch, Ilia …
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Journal article
Hyb-Seq for Flowering Plant Systematics
High-throughput DNA sequencing (HTS) presents great opportunities for plant systematics, yet genomic complexity needs to be reduced for HTS to be effectively applied. We highlight Hyb-Seq as a promising approach, especially in light of the recent development of probes enriching 353 low-copy nuclear genes from any flowering plant taxon. -
Journal article
A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number...Viruel, Juan ; Conejero, María ; Hidalgo, Oriane ; Pokorny, Lisa ; Powell, Robyn …