High-throughput genomic data in systematics and phylogenetics
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 …
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
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 …
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 …
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)
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 …
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 …
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)
Hybridization is a frequent and important force in plant evolution. Next-generation
sequencing (NGS) methods offer new possibilities for clade resolution and ambitious …
sequencing (NGS) methods offer new possibilities for clade resolution and ambitious …
MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes
Premise of the study: Targeted sequencing using next‐generation sequencing (NGS)
platforms offers enormous potential for plant systematics by enabling economical acquisition …
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 …
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 …
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 …
diverse array of plants; we focus on woody, aromatic, aquatic, and other chemically complex …