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 …

Chloroplot: an online program for the versatile plotting of organelle genomes

S Zheng, P Poczai, J Hyvönen, J Tang… - Frontiers in …, 2020 - frontiersin.org
Understanding the complexity of genomic structures and their unique architecture is linked
with the power of visualization tools used to represent these features. Such tools should be …

Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae

R Zhang, YH Wang, JJ **, GW Stull… - Systematic …, 2020 - academic.oup.com
Phylogenomic analyses have helped resolve many recalcitrant relationships in the
angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae …

Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae sl

DF Morales-Briones, G Kadereit, DT Tefarikis… - Systematic …, 2021 - academic.oup.com
Gene tree discordance in large genomic data sets can be caused by evolutionary processes
such as incomplete lineage sorting and hybridization, as well as model violation, and errors …

Target capture and genome skimming for plant diversity studies

FF Pezzini, G Ferrari, LL Forrest, ML Hart… - Applications in Plant …, 2023 - Wiley Online Library
Recent technological advances in long‐read high‐throughput sequencing and assembly
methods have facilitated the generation of annotated chromosome‐scale whole‐genome …

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

L Li, S Wang, H Wang, SK Sahu, B Marin, H Li… - Nature ecology & …, 2020 - nature.com
Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP
1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the …

Phylogenomic conflict analyses in the apple genus Malus sl reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex …

BB Liu, C Ren, M Kwak, RGJ Hodel… - Journal of Integrative …, 2022 - Wiley Online Library
Phylogenomic evidence from an increasing number of studies has demonstrated that
different data sets and analytical approaches often reconstruct strongly supported but …

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

O Maurin, A Anest, S Bellot, E Biffin… - American Journal of …, 2021 - Wiley Online Library
Premise To further advance the understanding of the species‐rich, economically and
ecologically important angiosperm order Myrtales in the rosid clade, comprising nine …

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 …

Defining coalescent genes: theory meets practice in organelle phylogenomics

JJ Doyle - Systematic biology, 2022 - academic.oup.com
The species tree paradigm that dominates current molecular systematic practice infers
species trees from collections of sequences under assumptions of the multispecies …