J. Chris Pires

J. Chris Pires
University of Missouri | Mizzou · Division of Biological Sciences

Ph.D.

About

366
Publications
100,544
Reads
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22,056
Citations
Introduction
Plant evolution and comparative genomics. Modeling networks and systems biology of polyploidy. Phylogenomics, chromosome evolution, and biogeography of Brassica (mustards). Systematics and genome evolution of Asparagales and related petaloid monocots. Origin of dioecy and sex chromosome evolution of Asparagus. Science education: student learning of phylogenetic tree thinking.
Additional affiliations
September 2011 - present
University of Missouri
Position
  • Professor (Associate)
August 2005 - October 2016
University of Missouri
Position
  • Professor (Full)
September 2001 - August 2005
University of Wisconsin–Madison
Position
  • PostDoc Position
Education
August 1994 - August 2000
August 1985 - May 1990

Publications

Publications (366)
Preprint
Fast interpolation-grid frameworks facilitate an efficient and flexible evaluation of higher-order predictions for any choice of parton distribution functions or value of the strong coupling $\alpha_s$. They constitute an essential tool for the extraction of parton distribution functions and Standard Model parameters, as well as studies of the depe...
Article
Full-text available
Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach...
Article
Full-text available
By modeling the homoeologous gene losses that occurred in fifty genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes or yeasts. We show that many of the events show a relative rate of duplicate ge...
Preprint
Full-text available
Allopolyploidy involves the hybridization of two evolutionary diverged species and the doubling of genomic material. Allopolyploids also exhibit homoeologous exchange that recombines, duplicate, or delete homoeologous regions of the newly formed genome. These kinds of changes to gene dosage are hypothesized to be constrained by selection to maintai...
Preprint
Full-text available
By modeling the homoeologous gene losses that occurred in fifty genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes or yeasts. The models suggest these events were nearly all allopolyploidies, wi...
Data
Cover Image for Molecular Biology and Evolution - Volume 38 Number 10 October 2021. Artist credit: Andi Kur
Article
Full-text available
Plant genomes demonstrate significant presence/absence variation (PAV) within a species, however the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer ho...
Article
Full-text available
Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet,...
Article
Full-text available
Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplicati...
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Full-text available
The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domesticat...
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Full-text available
The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood...
Article
Full-text available
Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales, ornate leaves, extended vegetative phase, and nutritional quality are some of the characters potentially selected by...
Article
Full-text available
Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better understanding of the underlying mechanisms leading to stabilization in the allopolyploid, the behavior of chromosom...
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Full-text available
Feral populations, those which successfully persist outside of cultivation or husbandry, provide unique opportunities to study the genomic impacts of domestication and local adaptation. We argue that by leveraging genomic resources designed for domestic counterparts, powerful phylogenetic and population genomic data collection and analyses can be d...
Article
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication....
Article
Full-text available
Allopolyploidization merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant” over the other subgenome, often being more highly expressed. Here, we “replayed the evolutionary tape” with six isogenic resynthesized Brassica napus allopolyploid lines and investigated...
Preprint
Full-text available
Morphotypes of Brassica oleracea are the result of a dynamic interaction between genes that regulate the transition between vegetative and reproductive stages and those that regulate leaf morphology and plant architecture. In kales ornate leaves, delayed flowering, and nutritional quality are some of the characters potentially selected by humans du...
Article
Full-text available
Premise: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placem...
Preprint
Full-text available
The members of the tribe Brassiceae share an ancient whole genome triplication (WGT), and plants in this tribe display extraordinarily high within-species morphological diversity. One proposed model for the formation of these hexaploid Brassiceae is that they result from a “two-step” pair of hybridizations. However, direct evidence supporting this...
Article
Full-text available
The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana ; (b) provide summaries from recent reports submi...
Preprint
Full-text available
Genome size of plants has long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplication...
Article
Full-text available
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on...
Article
Full-text available
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on...
Article
Full-text available
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on...
Article
Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy potentially...
Article
Full-text available
Crop domestication is a fascinating area of study, as shown by a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can be...
Preprint
Full-text available
This Report summarizes the proceedings of the 2019 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt with (I) new developments for high precision Standard Model calculations, (II) the sensitivity of parton distribution functions to the experimental inputs, (III) new developments in jet substructure techniques and a detailed examinat...
Preprint
Full-text available
Most plant species form symbioses with mycorrhizal fungi and this relationship is especially important for orchids. Fungi in the genera Tulasnella, Ceratobasidium, and Serendipita are critically important for orchid germination, growth and development. The goals of this study are to understand the phylogenetic relationships of mycorrhizal fungi and...
Preprint
Full-text available
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication....
Article
Full-text available
Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida),...
Preprint
Full-text available
One of the parental diploid genomes (subgenomes) in an allopolyploid often exhibits higher gene expression levels compared to the other subgenome(s) in the nucleus. However, the genetic basis and deterministic fate of subgenome expression dominance remains poorly understood. We examined the establishment of subgenome expression dominance in six iso...
Preprint
Full-text available
Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. However, while its sister family, Cleomaceae, has also been characterized by a WGD, its placement, as well as that...
Article
Full-text available
The extension of interpolation-grid frameworks for perturbative QCD calculations at next-to-next-to-leading order (NNLO) is presented for deep inelastic scattering (DIS) processes. A fast and flexible evaluation of higher-order predictions for any a posteriori choice of parton distribution functions (PDFs) or value of the strong coupling constant i...
Article
The extension of interpolation-grid frameworks for perturbative QCD calculations at next-to-next-to-leading order (NNLO) is presented for deep inelastic scattering (DIS) processes. A fast and flexible evaluation of higher-order predictions for any a posteriori choice of parton distribution functions (PDFs) or value of the strong coupling constant i...
Preprint
Crop domestication is a fascinating area of study, as evidenced by a multitude of recent reviews. Coupled with the increasing availability of genomic and phenomic resources in numerous crop species, insights from evolutionary biology will enable a deeper understanding of the genetic architecture and short-term evolution of complex traits, which can...
Preprint
Full-text available
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on...
Article
Full-text available
The measurement of the triple-differential dijet production cross section as a function of the average transverse momentum pT,avg, half the rapidity separation y*, and the boost yb of the two leading jets in the event enables a kinematical scan of the underlying parton momentum distributions. We compute for the first time the second-order perturbat...
Article
Full-text available
Premise: Environmentally controlled facilities, such as growth chambers, are essential tools for experimental research. Automated, low-cost, remote-monitoring hardware can greatly improve both reproducibility and maintenance. Methods and results: Using a Raspberry Pi computer, open-source software, environmental sensors, and a camera, we develop...
Article
Full-text available
Spinal Muscular Atrophy (SMA) is a monogenic neurodegenerative disorder and the leading genetic cause of infantile mortality. While several functions have been ascribed to the SMN (survival motor neuron) protein, their specific contribution to the disease has yet to be fully elucidated. We hypothesized that some, but not all, SMN homologues would r...
Article
Full-text available
Brassica napus, an allotetraploid crop, is hypothesized to be a hybrid from unknown varieties of Brassica rapa and Brassica oleracea. Despite the economic importance of B. napus, much is unresolved regarding its phylogenomic relationships, genetic structure, and diversification. Here we conduct a comprehensive study among diverse accessions from 18...
Preprint
The extension of interpolation-grid frameworks for perturbative QCD calculations at next-to-next-to-leading order (NNLO) is presented for deep inelastic scattering (DIS) processes. A fast and flexible evaluation of higher-order predictions for any a posteriori choice of parton distribution functions (PDFs) or value of the strong coupling constant i...
Preprint
Full-text available
Premise of the study: Environmentally controlled facilities, such as growth chambers, are essential tools for experimental research. Automated remote monitoring of such facilities with low-cost hardware can greatly improve both the reproducibility and the accurate maintenance of their conditions. Methods and Results: Using a Raspberry Pi computer,...
Article
Full-text available
Background RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – producing both a less dormant mucilaginous (M⁺) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compar...
Preprint
The future opportunities for high-density QCD studies with ion and proton beams at the LHC are presented. Four major scientific goals are identified: the characterisation of the macroscopic long wavelength Quark-Gluon Plasma (QGP) properties with unprecedented precision, the investigation of the microscopic parton dynamics underlying QGP properties...
Article
Duplication events are regarded as sources of evolutionary novelty, but our understanding of general trends for the long-term trajectory of additional genomic material is still lacking. Organisms with a history of whole genome duplication (WGD) offer a unique opportunity to study potential trends in the context of gene retention and/or loss, gene a...
Article
Full-text available
Premise of the Study We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot‐wide divergence times and rates of species diversification. Methods We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monoco...
Data
Appendix S1 Description of the statistical analyses of the RNA sequencing data, comparing effects of treatments, species and organs. Figure S1 Biomass production and Se and S accumulation by Stanleya pinnata and S. elata. The plants were grown from seed on agar with 0 or 20 μm sodium selenate. Figure S2 Overview of differential expression between...
Poster
Full-text available
Polyploidy is seen as a driver of both evolutionary innovation and ecological success. When the contributors to the polyploidy are distinct species (allopolyploidy), it has been claimed that the post-polyploidy retention of genes often favors one of the two subgenomes. However, most of the analyses of this pattern of "biased fractionation" are limi...
Data
Table S1 Assembly statistics. Table S2 Number of genes annotated and used in the analysis. Table S3 BUSCO results to assess the completeness of the pangenome assembly. Table S4 Gene PAV with respect to the synthetic and non‐synthetic accessions. Table S5 Number of uniquely present and absent genes in (a) non‐synthetics and (b) synthetics. Tabl...
Data
Data S2 Gene PAV of the flowering time regulators FLC, PHYA and GA3ox1 in the ERANET‐ASSYST B. napus diversity set. Swede lines are shown in red.
Data
Data S1 Results of the HE analysis across the Darmor‐bzh portion of the pangenome.
Article
Full-text available
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Article
Full-text available
The genus Aethionema is sister to the core Brassicaceae (including Arabidopsis thaliana) and thus has an important evolutionary position for comparative analyses. Aethionema arabicum (Brassicaceae) is emerging as a model to understand the evolution of various traits. We generated transcriptome data for seven Ae. arabicum genotypes across the specie...