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 …

Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches

EA Zimmer, J Wen - Journal of Systematics and Evolution, 2015 - Wiley Online Library
Single and low copy nuclear genes offer a larger number of, and more rapidly evolving,
characters than the chloroplast and nuclear ribosomal gene sequences that have dominated …

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 (NC‐cpDNA) sequences are the staple
data source of low‐level phylogeographic and phylogenetic studies of angiosperms. We …

A new taxonomic backbone for the infrageneric classification of the species‐rich genus Silene (Caryophyllaceae)

F Jafari, S Zarre, A Gholipour, F Eggens, RK Rabeler… - Taxon, 2020 - Wiley Online Library
The systematization of species in plant taxonomy based on the phylogenetic relationships
among them are of utmost importance and also very challenging in large genera. In those …

Evolving ideas on the origin and evolution of flowers: new perspectives in the genomic era

AS Chanderbali, BA Berger, DG Howarth, PS Soltis… - Genetics, 2016 - academic.oup.com
The origin of the flower was a key innovation in the history of complex organisms,
dramatically altering Earth's biota. Advances in phylogenetics, developmental genetics, and …

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

N García, RA Folk, AW Meerow, S Chamala… - Molecular Phylogenetics …, 2017 - Elsevier
Hybridization is a frequent and important force in plant evolution. Next-generation
sequencing (NGS) methods offer new possibilities for clade resolution and ambitious …

MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes

S Chamala, N García, GT Godden… - Applications in Plant …, 2015 - Wiley Online Library
Premise of the study: Targeted sequencing using next‐generation sequencing (NGS)
platforms offers enormous potential for plant systematics by enabling economical acquisition …

Sequencing and comparative analyses of the genomes of zoysiagrasses

H Tanaka, H Hirakawa, S Kosugi, S Nakayama… - DNA …, 2016 - academic.oup.com
Zoysia is a warm-season turfgrass, which comprises 11 allotetraploid species (2 n= 4 x= 40),
each possessing different morphological and physiological traits. To characterize the …

Geneious! Simplified genome skimming methods for phylogenetic systematic studies: A case study in Oreocarya (Boraginaceae)

LA Ripma, MG Simpson… - Applications in Plant …, 2014 - Wiley Online Library
• Premise of the study: As systematists grapple with how to best harness the power of next‐
generation sequencing (NGS), a deluge of review papers, methods, and analytical tools …

Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta

IE Jordon‐Thaden, AS Chanderbali… - Applications in plant …, 2015 - Wiley Online Library
Premise of the study: Here we present a series of protocols for RNA extraction across a
diverse array of plants; we focus on woody, aromatic, aquatic, and other chemically complex …