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 …

[HTML][HTML] Next-generation biology: sequencing and data analysis approaches for non-model organisms

RR da Fonseca, A Albrechtsen, GE Themudo… - Marine genomics, 2016 - Elsevier
As sequencing technologies become more affordable, it is now realistic to propose studying
the evolutionary history of virtually any organism on a genomic scale. However, when …

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 …

[HTML][HTML] Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Y Liu, MG Johnson, CJ Cox, R Medina, N Devos… - Nature …, 2019 - nature.com
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least
400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive …

Beyond Genera Palmarum: progress and prospects in palm systematics

WJ Baker, J Dransfield - Botanical Journal of the Linnean …, 2016 - academic.oup.com
The systematic biology of the palm family (Arecaceae) is probably better known than that of
any other tropical plant family of comparable size. As a result, the palms are now regarded …

[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 …

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

DF Morales‐Briones, A Liston, DC Tank - New Phytologist, 2018 - Wiley Online Library
Hybridization, incomplete lineage sorting, and phylogenetic error produce similar
incongruence patterns, representing a great challenge for phylogenetic reconstruction …

[HTML][HTML] Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

E Ogutcen, C Christe, K Nishii, N Salamin… - Molecular Phylogenetics …, 2021 - Elsevier
Abstract Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of
growth form and floral morphology that are associated with repeated adaptations to different …

[HTML][HTML] Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

JA Nicholls, RT Pennington, EJM Koenen… - Frontiers in Plant …, 2015 - frontiersin.org
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse
geographical and ecological settings; in neotropical rainforests there is growing evidence …

[HTML][HTML] Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

TLP Couvreur, AJ Helmstetter, EJM Koenen… - Frontiers in plant …, 2019 - frontiersin.org
Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic
reconstruction is becoming an important tool for plant systematics and evolution …