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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping and are able to reassemble the circular Plastomes from 47 datasets using GetOrganelle.
PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
Plastid Genome Annotator (PGA), a standalone command line tool that can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plasts, is introduced.
GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data
The GetOrganelle pipeline is an effective way for land plants to assemble the circular chloroplast genome, without needs for reference-guided scaffolding, gap filling nor start-end point closing.
A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies and reflects the phylogenetic structure that is consistently resolved.
Origin of angiosperms and the puzzle of the Jurassic gap
A study reconstructed angiosperm phylogeny on the basis of plastome data representing 2,351 angiosperm and 187 gymnosperm species, and dated the origin of crown angiosperms to be significantly earlier than the estimates based on fossil data.
Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics.
The robust phylogenetic backbone and time estimates the authors provide establish a framework for future comparative studies on rosaceous evolution and highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics.
Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication
It is proposed that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.
Plastid phylogenomic insights into the evolution of Caryophyllales.
Chromosomal evolution in Araliaceae and close relatives
Chromosome numbers of 45 accessions representing 16 genera and 37 species of Araliaceae are herein reported, of which 30 species and seven genera (Apiopetalum, Arthrophyllum, Delarbrea,…
Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae
The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification, although conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone.