Practical considerations for plant phylogenomics
MR McKain, MG Johnson… - Applications in plant …, 2018 - Wiley Online Library
The past decade has seen a major breakthrough in our ability to easily and inexpensively
sequence genome‐scale data from diverse lineages. The development of high‐throughput …
sequence genome‐scale data from diverse lineages. The development of high‐throughput …
[HTML][HTML] A guide to carrying out a phylogenomic target sequence capture project
T Andermann, MF Torres Jiménez… - Frontiers in …, 2020 - frontiersin.org
High-throughput DNA sequencing techniques enable time-and cost-effective sequencing of
large portions of the genome. Instead of sequencing and annotating whole genomes, many …
large portions of the genome. Instead of sequencing and annotating whole genomes, many …
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 …
DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the …
[HTML][HTML] 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 …
persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large …
Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches
Single and low copy nuclear genes offer a larger number of, and more rapidly evolving,
characters than the chloroplast and nuclear ribosomal gene sequences that have dominated …
characters than the chloroplast and nuclear ribosomal gene sequences that have dominated …
Bridging the micro‐and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above
Reconstructing phylogenetic relationships at the micro‐and macroevoutionary levels within
the same tree is problematic because of the need to use different data types and analytical …
the same tree is problematic because of the need to use different data types and analytical …
[HTML][HTML] Phylogenomic mining of the mints reveals multiple mechanisms contributing to the evolution of chemical diversity in Lamiaceae
The evolution of chemical complexity has been a major driver of plant diversification, with
novel compounds serving as key innovations. The species-rich mint family (Lamiaceae) …
novel compounds serving as key innovations. The species-rich mint family (Lamiaceae) …
Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages
Premise Discordance between nuclear and organellar phylogenies (cytonuclear
discordance) is a well‐documented phenomenon at shallow evolutionary levels but has …
discordance) is a well‐documented phenomenon at shallow evolutionary levels but has …
Retrieval of hundreds of nuclear loci from herbarium specimens
Herbaria are unparalleled collections of biodiversity information representing the world's
flora. However, this treasure has remained largely inaccessible to genetic studies, frequently …
flora. However, this treasure has remained largely inaccessible to genetic studies, frequently …
A new classification of Carex (Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree
T Villaverde, P Jimenez-Mejias… - Botanical Journal of …, 2020 - academic.oup.com
The field of systematics is experiencing a new molecular revolution driven by the increased
availability of high-throughput sequencing technologies. As these techniques become more …
availability of high-throughput sequencing technologies. As these techniques become more …