Green giant—a tiny chloroplast genome with mighty power to produce highvalue proteins: history and phylogeny

H Daniell, S Jin, XG Zhu… - Plant biotechnology …, 2021 - Wiley Online Library
Freeliving cyanobacteria were entrapped by eukaryotic cells~ 2 billion years ago, ultimately
giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was …

Plant DNA barcoding: from gene to genome

X Li, Y Yang, RJ Henry, M Rossetto, Y Wang… - Biological …, 2015 - Wiley Online Library
ABSTRACT DNA barcoding is currently a widely used and effective tool that enables rapid
and accurate identification of plant species; however, none of the available loci work across …

HybPiper: Extracting coding sequence and introns for phylogenetics from highthroughput sequencing reads using target enrichment

MG Johnson, EM Gardner, Y Liu… - Applications in plant …, 2016 - Wiley Online Library
Premise of the study: Using sequence data generated via target enrichment for
phylogenetics requires reassembly of highthroughput sequence reads into loci, presenting …

From barcodes to genomes: extending the concept of DNA barcoding

E Coissac, PM Hollingsworth, S Lavergne, P Taberlet - 2016 - Wiley Online Library
DNA barcoding has had a major impact on biodiversity science. The elegant simplicity of
establishing massive scale databases for a few barcode loci is continuing to change our …

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 …

[HTML][HTML] From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

BR Ruhfel, MA Gitzendanner, PS Soltis… - BMC evolutionary …, 2014 - Springer
Background Next-generation sequencing has provided a wealth of plastid genome
sequence data from an increasingly diverse set of green plants (Viridiplantae). Although …

HybSeq: Combining target enrichment and genome skimming for plant phylogenomics

K Weitemier, SCK Straub, RC Cronn… - Applications in plant …, 2014 - Wiley Online Library
• Premise of the study: HybSeq, the combination of target enrichment and genome
skimming, allows simultaneous data collection for lowcopy nuclear genes and highcopy …

High-throughput genomic data in systematics and phylogenetics

EM Lemmon, AR Lemmon - Annual Review of Ecology …, 2013 - annualreviews.org
High-throughput genomic sequencing is rapidly changing the field of phylogenetics by
decreasing the cost and increasing the quantity and rate of data collection by several orders …

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 genomescale data from diverse lineages. The development of highthroughput …

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV

J Shaw, HL Shafer, OR Leonard… - American Journal of …, 2014 - Wiley Online Library
• Premise of the study: Noncoding chloroplast DNA (NCcpDNA) sequences are the staple
data source of lowlevel phylogeographic and phylogenetic studies of angiosperms. We …