16 Works

Data from: Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells

Megan M. Augustin, Dan R. Ruzicka, Ashutosh K. Shukla, Courtney M. Starks, Mark O'Neil-Johnson, Michael R. McKain, Bradley S. Evans, Matthew D. Barrett, Ann Smithson, Gane Ka-Shu Wong, Michael K. Deyholos, Patrick P. Edger, J. Chris Pires, James H. Leebens-Mack, Dave A. Mann, Toni M. Kutchan & Matt D. Barrett
Steroid alkaloids have been shown to elicit a wide range of pharmacological effects that include anticancer and antifungal activities. Understanding the biosynthesis of these molecules is essential to bioengineering for sustainable production. Herein, we investigate the biosynthetic pathway to cyclopamine, a steroid alkaloid that shows promising antineoplastic activities. Supply of cyclopamine is limited, as the current source is solely derived from wild collection of the plant Veratrum californicum. To elucidate the early stages of the...

Data from: Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants

Dieter Hackenberg, Michael McKain, Soon-Goo Lee, Swarup Roy Choudhury, Tyler McCann, Spencer Schreier, Alex Harkess, J. Chris Pires, Gane Ka-Shu Wong, Joseph Jez, Elizabeth Kellogg, Sona Pandey, Soon Goo Lee, Joseph M. Jez, Michael R. McKain & Elizabeth A. Kellogg
Signaling pathways regulated by heterotrimeric G-proteins exist in all eukaryotes. The regulator of G-protein signaling (RGS) proteins are key interactors and critical modulators of the Gα protein of the heterotrimer. However, while G-proteins are widespread in plants, RGS proteins have been reported to be missing from the entire monocot lineage, with two exceptions. A single amino acid substitution-based adaptive coevolution of the Gα:RGS proteins was proposed to enable the loss of RGS in monocots. We...

Data from: A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

Michael R. McKain, Haibao Tang, Joel R. McNeal, Saravanaraj Ayyampalayam, Jerrold I. Davis, Claude W. DePamphilis, Thomas J. Givnish, J. Chris Pires, Dennis Wm. Stevenson & Jim H. Leebens-Mack
Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intra-genomic syntenic blocks. Three such whole genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein coding sequences. The timing of...

Data from: Annual understory plant recovery dynamics in a temperate woodland mosaic during a decade of ecological restoration

J. Leighton Reid, Nels J. Holmberg, Matthew Albrecht, Sandra Arango-Caro, Olivia Hajek, Quinn Long & James Trager
Temperate woodlands are one of the world’s ecosystems in greatest need of ecological restoration, but relatively little is known about their floristic recovery dynamics over decadal timescales. From 2000 to 2012, we monitored understory plant communities in a woodland mosaic in Missouri, USA, as it underwent restoration via prescribed, dormant-season burning and mechanical thinning of red cedar (Juniperus virginiana) and exotic shrubs. Native species richness increased linearly by 36% over this time period, driven primarily...

Data from: Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

Mario Vallejo-Marin, Arielle M. Cooley, Michelle Yuequi Lee, Madison Folmer, Michael R. McKain & Joshua Robert Puzey
PREMISE OF THE STUDY: Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for “maternal-excess” crosses where the mother has a higher ploidy than the father. Here we investigated the evolutionary origins of Mimulus peregrinus, an allohexaploid recently derived from the triploid M. ×robertsii, to determine whether reproductive asymmetry has shaped the formation of this new species. METHODS:...

Data from: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower

Patrick P. Edger, Ronald D. Smith, Michael R. McKain, Arielle M. Cooley, Mario Vallejo-Marin, Yao-Wu Yuan, Adam J. Bewick, Lexiang Ji, Adrian E. Platts, Megan J. Bowman, Kevin Childs, Jacob D. Washburn, Robert Schmitz, Gregory D. Smith, J. Chris Pires & Joshua R. Puzey
Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural,...

Data from: Population genetics of Setaria viridis, a new model system

Pu Huang, Maximilian Feldman, Stephan Schroder, Bochra A. Bahri, Xianmin Diao, Hui Zhi, Matt Estep, Ivan Baxter, Katrien M. Devos & Elizabeth A. Kellogg
An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production, and small diploid genome, among other characters. However, remarkably little...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Data from: Retrotransposon proliferation coincident with the evolution of dioecy in asparagus

Alex Harkess, Francesco Mercati, Loredana Abbate, Michael McKain, J. Chris Pires, Tea Sala, Francesco Sunseri, Agostino Falavigna & Jim Leebens-Mack
Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or...

Data from: Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function

David M. Goad, Chuanmei Zhu & Elizabeth A. Kellogg
CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12–13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive...

Data from: High fidelity detection of crop biomass QTL from low-cost imaging in the field

Darshi Banan, Rachel E. Paul, Max J. Feldman, Mark W. Holmes, Hannah Schlake, Ivan Baxter, Hui Jiang & Andrew D.B. Leakey
Field-based, rapid, and non-destructive techniques for assessing plant productivity are needed to accelerate the discovery of genotype-to-phenotype relationships in next-generation biomass grass crops. The use of hemispherical imaging and light attenuation modeling was evaluated against destructive harvest measures with respect to their ability to accurately capture phenotypic and genotypic relationships in a field-grown grass crop. Plant area index (PAI) estimated from below-canopy hemispherical images, as well as a suite of thirteen traits assessed by manual...

Data from: Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium

Christine A. McAllister, Michael R. McKain, Mao Li, Bess Bookout & Elizabeth A. Kellogg
Herbaria contain a cumulative sample of the world’s flora, assembled by thousands of people over several hundred years. Recent advances in computation, DNA sequencing, and image manipulation have allowed us to capitalize on this resource. Using herbarium material, we conducted a species-level analysis of a major clade in the grass tribe Andropogoneae, which includes the dominant species of the world’s grasslands, from the genera Andropogon, Schizachyrium, Hyparrhenia, and other groups. We imaged 188 of the...

Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses

Matheus Bianconi, Jan Hackel, Maria Vorontsova, Adriana Alberti, Watchara Arthan, Sean Burke, Melvin Duvall, Elizabeth Kellogg, Sébastien Lavergne, Michael McKain, Alexandre Meunier, Colin Osborne, Paweena Traiperm, Pascal-Antoine Christin & Guillaume Besnard
C4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C4 lineages is Andropogoneae, a group of ~ 1,200 grass species that includes some of the world's most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C4 evolution in the group have compared a few model C4 plants to distantly related...

Data from: Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens

Saman Saeidi, Michael R. McKain & Elizabeth A. Kellogg
Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for...

Data from: Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae)

Michael R. McKain, Joel R. McNeal, P. Roxanne Kellar, Luis E. Eguiarte, J. Chris Pires, James Leebens-Mack & Jim Leebens-Mack
PREMISE OF THE STUDY: Yucca species are ideal candidates for the study of coevolution due to the obligate mutualism they form with yucca moth pollinators (genera Tegeticula and Parategeticula). Yuccas are not the only species to exhibit a mutualism with yucca moths; the genus Hesperoyucca is pollinated by the California yucca moth (Tegeticula maculata). Relationships among yuccas, Hesperoyucca, and other members of subfamily Agavoideae are necessary to understand the evolution of this unique pollination syndrome....

Data from: Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

Patrick P. Edger, Jocelyn C. Hall, Alex Harkess, Michelle Tang, Jill Coombs, Setareh Mohammadin, M. Eric Schranz, Zhiyong Xiong, James Leebens-Mack, Blake C. Meyers, Kenneth J. Systma, Marcus A. Koch, Ihsan A. Al-Shehbaz, J. Chris Pires & Kenneth J. Sytsma
PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS - We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp...

Registration Year

  • 2020
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  • 2018
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  • 2014

Resource Types

  • Dataset


  • Donald Danforth Plant Science Center
  • University of Georgia
  • University of Missouri
  • University of Alberta
  • Washington University in St. Louis
  • University of Wisconsin-Madison
  • College of William & Mary
  • University of Stirling
  • University of Illinois at Urbana Champaign
  • Missouri Botanical Garden