Phylogenomics and the flowering plant tree of life

C Guo, Y Luo, LM Gao, TS Yi, HT Li… - Journal of Integrative …, 2023 - Wiley Online Library
The advances accelerated by next‐generation sequencing and long‐read sequencing
technologies continue to provide an impetus for plant phylogenetic study. In the past …

Hyb-Seq for flowering plant systematics

S Dodsworth, L Pokorny, MG Johnson, JT Kim… - Trends in Plant …, 2019 - Elsevier
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 …

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

WJ Baker, P Bailey, V Barber, A Barker… - Systematic …, 2022 - academic.oup.com
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 …

A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

MG Johnson, L Pokorny, S Dodsworth… - Systematic …, 2019 - academic.oup.com
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 …

A new classification of Cyperaceae (Poales) supported by phylogenomic data

I Larridon, AR Zuntini, É Léveillé‐Bourret… - … of Systematics and …, 2021 - Wiley Online Library
Cyperaceae (sedges) are the third largest monocot family and are of considerable economic
and ecological importance. Sedges represent an ideal model family to study evolutionary …

[HTML][HTML] Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms

GE Brewer, JJ Clarkson, O Maurin, AR Zuntini… - Frontiers in plant …, 2019 - frontiersin.org
The world's herbaria collectively house millions of diverse plant specimens, including
endangered or extinct species and type specimens. Unlocking genetic data from the …

Highly resolved papilionoid legume phylogeny based on plastid phylogenomics

IS Choi, D Cardoso, LP De Queiroz… - Frontiers in Plant …, 2022 - frontiersin.org
Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest
subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily …

Tackling rapid radiations with targeted sequencing

I Larridon, T Villaverde, AR Zuntini, L Pokorny… - Frontiers in plant …, 2020 - frontiersin.org
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 …

Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

H Hale, EM Gardner, J Viruel, L Pokorny… - Applications in plant …, 2020 - Wiley Online Library
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 …

Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

WJ Baker, S Dodsworth, F Forest, SW Graham… - 2021 - ttu-ir.tdl.org
The unveiling of the angiosperm (flowering plant) tree of life over the past three decades has
been one of the great success stories of modern plant biology. Flowering plants underpin …