Journal ArticleDOI
Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.
TLDR
The utility of genome skimming is demonstrated through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae) and the effect of divergence on reference-guided plastome assembly is addressed.Citations
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PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
TL;DR: 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.
Journal ArticleDOI
From algae to angiosperms–inferring the phylogeny of green plants ( Viridiplantae ) from 360 plastid genomes
Brad R. Ruhfel,Matthew A. Gitzendanner,Matthew A. Gitzendanner,Pamela S. Soltis,Pamela S. Soltis,Douglas E. Soltis,Douglas E. Soltis,J. Gordon Burleigh +7 more
TL;DR: The limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data are explored and the importance of exploring the effects of different partitioning and character coding strategies is emphasized.
Journal ArticleDOI
Plann: A Command-Line Application for Annotating Plastome Sequences
TL;DR: Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastom, ready to use in other software pipelines and can be easily rerun as a draft plastsome is improved.
Journal ArticleDOI
Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics
Kevin Weitemier,Shannon C. K. Straub,Richard Cronn,Mark Fishbein,Roswitha Schmickl,Angela McDonnell,Aaron Liston +6 more
TL;DR: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics.
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GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data
TL;DR: 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.
References
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Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
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