Telling plant species apart with DNA: from barcodes to genomes

PM Hollingsworth, DZ Li… - … Transactions of the …, 2016 - royalsocietypublishing.org
Land plants underpin a multitude of ecosystem functions, support human livelihoods and
represent a critically important component of terrestrial biodiversity—yet many tens of …

Practical considerations for plant phylogenomics

MR McKain, MG Johnson… - Applications in plant …, 2018 - Wiley Online Library
The past decade has seen a major breakthrough in our ability to easily and inexpensively
sequence genome‐scale data from diverse lineages. The development of high‐throughput …

BlobToolKit–interactive quality assessment of genome assemblies

R Challis, E Richards, J Rajan… - G3: Genes …, 2020 - academic.oup.com
Reconstruction of target genomes from sequence data produced by instruments that are
agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether …

OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: expanded toolkit for the graphical visualization of organellar genomes

S Greiner, P Lehwark, R Bock - Nucleic acids research, 2019 - academic.oup.com
Organellar (plastid and mitochondrial) genomes play an important role in resolving
phylogenetic relationships, and next-generation sequencing technologies have led to a …

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

JJ Jin, 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 …

A comprehensive phylogenomic platform for exploring the angiosperm tree of life

WJ Baker, P Bailey, V Barber, A Barker… - Systematic …, 2022 - academic.oup.com
The tree of life is the fundamental biological roadmap for navigating the evolution and
properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering …

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 …

Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms

GE Brewer, JJ Clarkson, O Maurin, AR Zuntini… - Frontiers in plant …, 2019 - frontiersin.org
The world's herbaria collectively house millions of diverse plant specimens, including
endangered or extinct species and type specimens. Unlocking genetic data from the …

Genome skimming herbarium specimens for DNA barcoding and phylogenomics

CX Zeng, PM Hollingsworth, J Yang, ZS He, ZR Zhang… - Plant Methods, 2018 - Springer
Background The world's herbaria contain millions of specimens, collected and named by
thousands of researchers, over hundreds of years. However, this treasure has remained …

Hybridization and hybrid speciation under global change

M Vallejo‐Marín, SJ Hiscock - New Phytologist, 2016 - Wiley Online Library
An unintended consequence of global change is an increase in opportunities for
hybridization among previously isolated lineages. Here we illustrate how global change can …