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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
TLDR
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
TLDR
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
TLDR
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.
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants
TLDR
It is proposed that ITS/ITS2 should be incorporated into the core barcode for seed plants, because in cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplified and sequence this subset of the marker.
Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses
TLDR
The results reveal that phylogenomics based on organelle genome sequencing lights the species identification—organelle-scale “barcodes”, and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.
The science and economics of ex situ plant conservation.
Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics.
TLDR
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.
Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot.
TLDR
The high genetic divergence, long-term isolation and ecological differentiation suggest a scenario of cryptic speciation in T. wallichiana associated with geological and climatic changes in the HHM, and challenges the notion of general population 'contraction' during the last glaciation in the region.
DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species
TLDR
Using the proposed DNA barcode, a technical system can be established to rapidly and reliably identify Taxus species in Eurasia for conservation protection and for monitoring illegal trade.
Plastid phylogenomic insights into the evolution of Caryophyllales.
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