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 …

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

JJ **, WB Yu, JB Yang, Y Song, CW DePamphilis… - Genome biology, 2020 - Springer
GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from
whole genome sequencing data. It recruits organelle-associated reads using a modified …

An updated tribal classification of Lamiaceae based on plastome phylogenomics

F Zhao, YP Chen, Y Salmaki, BT Drew, TC Wilson… - BMC biology, 2021 - Springer
Background A robust molecular phylogeny is fundamental for develo** a stable
classification and providing a solid framework to understand patterns of diversification …

Angiosperms at the edge: Extremity, diversity, and phylogeny

RA Folk, CM Siniscalchi, DE Soltis - Plant, Cell & Environment, 2020 - Wiley Online Library
A hallmark of flowering plants is their ability to invade some of the most extreme and
dynamic habitats, including cold and dry biomes, to a far greater extent than other land …

GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data

JJ Jian, WB Yu, JB Yang, Y Song, TS Yi, DZ Li - BioRxiv, 2018 - biorxiv.org
Background: Chloroplast genes and genomes are the most important genomic data for plant
phylogeny and DNA barcoding. Since the rapid development of high throughput sequencing …

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 …

Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Q Qiao, PP Edger, L Xue, L Qiong, J Lu… - Proceedings of the …, 2021 - pnas.org
Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and
applied research in recent years. In total, the genomes of five different species have been …

Phylogeny, biogeography and diversification of the mining bee family Andrenidae

S Bossert, TJ Wood, S Patiny, D Michez… - Systematic …, 2022 - Wiley Online Library
The mining bees (Andrenidae) are a major bee family of over 3000 described species with a
nearly global distribution. They are a particularly significant component of northern …

Plastid phylogenomic insights into the evolution of Caryophyllales

G Yao, JJ **, HT Li, JB Yang, VS Mandala… - Molecular Phylogenetics …, 2019 - Elsevier
The Caryophyllales includes 40 families and 12,500 species, representing a large and
diverse clade of angiosperms. Collectively, members of the clade grow on all continents and …

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 …