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 …

Dynamic genome evolution in a model fern

DB Marchant, G Chen, S Cai, F Chen, P Schafran… - Nature Plants, 2022 - nature.com
The large size and complexity of most fern genomes have hampered efforts to elucidate
fundamental aspects of fern biology and land plant evolution through genome-enabled …

WGDI: a user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

P Sun, B Jiao, Y Yang, L Shan, T Li, X Li, Z Xi, X Wang… - Molecular plant, 2022 - cell.com
Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has
been detected in most major lineages of living organisms on Earth. To clarify the complex …

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

FW Li, P Brouwer, L Carretero-Paulet, S Cheng… - Nature plants, 2018 - nature.com
Ferns are the closest sister group to all seed plants, yet little is known about their genomes
other than that they are generally colossal. Here, we report on the genomes of Azolla …

Unlocking plant metabolic diversity: A (pan)-genomic view

X Zhou, Z Liu - Plant Communications, 2022 - cell.com
Plants produce a remarkable diversity of structurally and functionally diverse natural
chemicals that serve as adaptive compounds throughout their life cycles. However …

Evolution of complex genome architecture in gymnosperms

T Wan, Y Gong, Z Liu, YD Zhou, C Dai, Q Wang - GigaScience, 2022 - academic.oup.com
Gymnosperms represent an ancient lineage that diverged from early spermatophytes during
the Devonian. The long fossil records and low diversity in living species prove their complex …

The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence

X Huang, W Wang, T Gong, D Wickell, LY Kuo… - Nature Plants, 2022 - nature.com
To date, little is known about the evolution of fern genomes, with only two small genomes
published from the heterosporous Salviniales. Here we assembled the genome of Alsophila …

Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids

Y Liu, B Wang, S Shu, Z Li, C Song, D Liu, Y Niu… - Nature …, 2021 - nature.com
Abstract Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales,
represents an important early-diverging eudicot lineage with diverse medicinal applications …

Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the baker's yeast lineage

M Marcet-Houben, T Gabaldón - PLoS biology, 2015 - journals.plos.org
Whole-genome duplications have shaped the genomes of several vertebrate, plant, and
fungal lineages. Earlier studies have focused on establishing when these events occurred …

Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes

C Li, D Wickell, LY Kuo, X Chen, B Nie… - Proceedings of the …, 2024 - National Acad Sciences
Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of
life, having split from heterosporous lycophytes (Selaginella and Isoetes)~ 400 Mya …