Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Green giant—a tiny chloroplast genome with mighty power to produce highvalue proteins: history and phylogeny

H Daniell, S Jin, XG Zhu… - Plant biotechnology …, 2021 - Wiley Online Library
Freeliving cyanobacteria were entrapped by eukaryotic cells~ 2 billion years ago, ultimately
giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was …

[HTML][HTML] One thousand plant transcriptomes and the phylogenomics of green plants

Nature, 2019 - nature.com
Green plants (Viridiplantae) include around 450,000–500,000 species, of great diversity and
have important roles in terrestrial and aquatic ecosystems. Here, as part of the One …

[HTML][HTML] Plastid phylogenomic insights into relationships of all flowering plant families

HT Li, Y Luo, L Gan, PF Ma, LM Gao, JB Yang, J Cai… - BMC biology, 2021 - Springer
Background Flowering plants (angiosperms) are dominant components of global terrestrial
ecosystems, but phylogenetic relationships at the familial level and above remain only …

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

AM Kozlov, D Darriba, T Flouri, B Morel… - …, 2019 - academic.oup.com
Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …

Origin of angiosperms and the puzzle of the Jurassic gap

HT Li, TS Yi, LM Gao, PF Ma, T Zhang, JB Yang… - Nature plants, 2019 - nature.com
Angiosperms are by far the most species-rich clade of land plants, but their origin and early
evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny …

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 …

[PDF][PDF] Genomes of subaerial Zygnematophyceae provide insights into land plant evolution

S Cheng, W Xian, Y Fu, B Marin, J Keller, T Wu, W Sun… - Cell, 2019 - cell.com
The transition to a terrestrial environment, termed terrestrialization, is generally regarded as
a pivotal event in the evolution and diversification of the land plant flora that changed the …

The Plant DNA C-values database (release 7.1)

J Pellicer, IJ Leitch - The new phytologist, 2020 - JSTOR
In recent decades, interest in plant genome size (ie the total amount of DNA in the
unreplicated haploid nucleus; Greilhuber et al., 2005) has been growing exponentially as …

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 …