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The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel Nov 2019

The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that ...


Beyond The Black Box: Promoting Mathematical Collaborations For Elucidating Interactions In Soil Ecology, Alison E. Bennett, Lori Biederman, Matthew Warren, Et Al. Jul 2019

Beyond The Black Box: Promoting Mathematical Collaborations For Elucidating Interactions In Soil Ecology, Alison E. Bennett, Lori Biederman, Matthew Warren, Et Al.

Ecology, Evolution and Organismal Biology Publications

Understanding soil systems is critical because they form the structural and nutritional foundation for plants and thus every terrestrial habitat and agricultural system. In this paper, we encourage increased use of mathematical models to drive forward understanding of interactions in soil ecological systems. We discuss several distinctive features of soil ecosystems and empirical studies of them. We explore some perceptions that have previously deterred more extensive use of models in soil ecology and some advances that have already been made using models to elucidate soil ecological interactions. We provide examples where mathematical models have been used to test the plausibility ...


Monarch Butterfly Host Plant (Milkweed Asclepias Spp.) Abundance Varies By Habitat Type Across 98 Prairies, Andrew D. Kaul, Brian J. Wilsey Jun 2019

Monarch Butterfly Host Plant (Milkweed Asclepias Spp.) Abundance Varies By Habitat Type Across 98 Prairies, Andrew D. Kaul, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

The decline in migratory monarch butterflies (Danaus plexippus) over the past 20 years has been attributed to several drivers, including loss of their host plants (milkweeds Asclepias spp.). This has sparked widespread interest in milkweed ecology and restoration. We developed a model on environmental and habitat type variables to predict milkweed abundance by sampling 93 prairie plantings (47 conservation plantings and 46 roadsides) and five unplowed prairie remnants throughout the state of Iowa, U.S.A. Milkweeds were censused in 10‐25 random locations within each site, and data on plant diversity, age of planting, soil characteristics, and management were ...


Interacting Stressors Matter: Diet Quality And Virus Infection In Honeybee Health, Adam G. Dolezal, Jimena Carrillo-Tripp, Timothy M. Judd, W. Allen Miller, Bryony C. Bonning, Amy L. Toth Feb 2019

Interacting Stressors Matter: Diet Quality And Virus Infection In Honeybee Health, Adam G. Dolezal, Jimena Carrillo-Tripp, Timothy M. Judd, W. Allen Miller, Bryony C. Bonning, Amy L. Toth

Ecology, Evolution and Organismal Biology Publications

Honeybee population declines have been linked to multiple stressors, including reduced diet diversity and increased exposure to understudied viral pathogens. Despite interest in these factors, few experimental studies have explored the interaction between diet diversity and viral infection in honeybees. Here, we used a mixture of laboratory cage and small semi-field nucleus hive experiments to determine how these factors interact. In laboratory experiments, we found that high-quality diets (polyfloral pollen and high-quality single-source pollen) have the potential to reduce mortality in the face of infection with Israeli acute paralysis virus (IAPV). There was a significant interaction between diet and virus ...


Mycorrhizal Colonization And Its Relationship With Plant Performance Differs Between Exotic And Native Grassland Plant Species, Aleksandra Checinska Sielaff, H. Wayne Polley, Andres Fuentes-Ramirez, Kirsten Hofmockel, Brian J. Wilsey Jan 2019

Mycorrhizal Colonization And Its Relationship With Plant Performance Differs Between Exotic And Native Grassland Plant Species, Aleksandra Checinska Sielaff, H. Wayne Polley, Andres Fuentes-Ramirez, Kirsten Hofmockel, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

Many grasslands have been transformed by exotic species with potentially novel ecological interactions. We hypothesized that exotic and native plant species differ, on average, in their percentage mycorrhizal colonization, and that mycorrhizal colonization is positively related to plant performance in the field. We compared colonization by arbuscular mycorrhizae (AM) fungi in perennial native and exotic species that were paired phylogenetically and by functional groups and grown under a common environment in field plots in Central Texas, USA. Roots were collected from plants in monoculture plots, stained, and percent colonization was assessed with a microscope. Aboveground biomass and dominance in mixture ...


Mechanisms Underlying Limited Soil Carbon Gains In Perennial And Cover‐Cropped Bioenergy Systems Revealed By Stable Isotopes, Chenglong Ye, Steven J. Hall Jan 2019

Mechanisms Underlying Limited Soil Carbon Gains In Perennial And Cover‐Cropped Bioenergy Systems Revealed By Stable Isotopes, Chenglong Ye, Steven J. Hall

Ecology, Evolution and Organismal Biology Publications

Removal of biomass for bioenergy production may decrease soil organic carbon. While perennials or cover‐cropped grains often have greater root production than annual grain crops, they variably impact soil carbon and underlying mechanisms remain unclear. We used high‐frequency measurements of soil respiration and natural abundance carbon stable isotopes to differentiate respiration sources, pool sizes, and decomposition rate constants during a 10 month incubation of soils collected to 1 m depth from a 10 year old field experiment in Iowa, United States. Conversion of corn–soybean rotations to reconstructed prairies or addition of a rye cover crop to continuous ...


Unraveling Cis And Trans Regulatory Evolution During Cotton Domestication, Ying Bao, Guanjing Hu, Corrinne E. Grover, Justin Conover, Daojun Yuan, Jonathan F. Wendel Jan 2019

Unraveling Cis And Trans Regulatory Evolution During Cotton Domestication, Ying Bao, Guanjing Hu, Corrinne E. Grover, Justin Conover, Daojun Yuan, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Cis and trans regulatory divergence underlies phenotypic and evolutionary diversification. Relatively little is understood about the complexity of regulatory evolution accompanying crop domestication, particularly for polyploid plants. Here, we compare the fiber transcriptomes between wild and domesticated cotton (Gossypium hirsutum) and their reciprocal F1 hybrids, revealing genome-wide (~15%) and often compensatory cis and trans regulatory changes under divergence and domestication. The high level of trans evolution (54%–64%) observed is likely enabled by genomic redundancy following polyploidy. Our results reveal that regulatory variation is significantly associated with sequence evolution, inheritance of parental expression patterns, co-expression gene network properties, and genomic ...


The Chromosome-Scale Reference Genome Of Black Pepper Provides Insight Into Piperine Biosynthesis, Lisong Hu, Zhongping Xu, Maojun Wang, Rui Fan, Daojun Yuan, Baoduo Wu, Huasong Wu, Xiaowei Qin, Lin Yan, Lehe Tan, Soonliang Sim, Wen Li, Christopher A. Saski, Henry Daniell, Jonathan F. Wendel, Keith Lindsey, Xianlong Zhang, Chaoyun Hao, Shuangxia Jin Jan 2019

The Chromosome-Scale Reference Genome Of Black Pepper Provides Insight Into Piperine Biosynthesis, Lisong Hu, Zhongping Xu, Maojun Wang, Rui Fan, Daojun Yuan, Baoduo Wu, Huasong Wu, Xiaowei Qin, Lin Yan, Lehe Tan, Soonliang Sim, Wen Li, Christopher A. Saski, Henry Daniell, Jonathan F. Wendel, Keith Lindsey, Xianlong Zhang, Chaoyun Hao, Shuangxia Jin

Ecology, Evolution and Organismal Biology Publications

Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the ...


More Salt, Please: Global Patterns, Responses And Impacts Of Foliar Sodium In Grasslands, E. T. Borer, E. M. Lind, J. Firn, E. W. Seabloom, T. M. Anderson, E. S. Bakker, L. A. Biederman, K. J. La Pierre, A. S. Macdougall, J. L. Moore, A. C. Risch, M. Schutz, C. J. Stevens Jan 2019

More Salt, Please: Global Patterns, Responses And Impacts Of Foliar Sodium In Grasslands, E. T. Borer, E. M. Lind, J. Firn, E. W. Seabloom, T. M. Anderson, E. S. Bakker, L. A. Biederman, K. J. La Pierre, A. S. Macdougall, J. L. Moore, A. C. Risch, M. Schutz, C. J. Stevens

Ecology, Evolution and Organismal Biology Publications

Sodium is unique among abundant elemental nutrients, because most plant species do not require it for growth or development, whereas animals physiologically require sodium. Foliar sodium influences consumption rates by animals and can structure herbivores across landscapes. We quantified foliar sodium in 201 locally abundant, herbaceous species representing 32 families and, at 26 sites on four continents, experimentally manipulated vertebrate herbivores and elemental nutrients to determine their effect on foliar sodium. Foliar sodium varied taxonomically and geographically, spanning five orders of magnitude. Site‐level foliar sodium increased most strongly with site aridity and soil sodium; nutrient addition weakened the relationship ...


Spectral Heterogeneity Predicts Local-Scale Gamma And Beta Diversity Of Mesic Grasslands, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay Jan 2019

Spectral Heterogeneity Predicts Local-Scale Gamma And Beta Diversity Of Mesic Grasslands, H. Wayne Polley, Chenghai Yang, Brian J. Wilsey, Philip A. Fay

Ecology, Evolution and Organismal Biology Publications

Plant species diversity is an important metric of ecosystem functioning, but field assessments of diversity are constrained in number and spatial extent by labor and other expenses. We tested the utility of using spatial heterogeneity in the remotely-sensed reflectance spectrum of grassland canopies to model both spatial turnover in species composition and abundances (β diversity) and species diversity at aggregate spatial scales (γ diversity). Shannon indices of γ and β diversity were calculated from field measurements of the number and relative abundances of plant species at each of two spatial grains (0.45 m2 and 35.2 m2 ...


Intergenomic Gene Transfer In Diploid And Allopolyploid Gossypium, Nan Zhao, Corrinne E. Grover, Zhiwen Chen, Jonathan F. Wendel, Jinping Hua Jan 2019

Intergenomic Gene Transfer In Diploid And Allopolyploid Gossypium, Nan Zhao, Corrinne E. Grover, Zhiwen Chen, Jonathan F. Wendel, Jinping Hua

Ecology, Evolution and Organismal Biology Publications

Background: Intergenomic gene transfer (IGT) between nuclear and organellar genomes is a common phenomenon during plant evolution. Gossypium is a useful model to evaluate the genomic consequences of IGT for both diploid and polyploid species. Here, we explore IGT among nuclear, mitochondrial, and plastid genomes of four cotton species, including two allopolyploids and their model diploid progenitors (genome donors, G. arboreum: A2 and G. raimondii: D5).

Results: Extensive IGT events exist for both diploid and allotetraploid cotton (Gossypium) species, with the nuclear genome being the predominant recipient of transferred DNA followed by the mitochondrial genome. The nuclear genome has integrated ...


Leaf Nutrients, Not Specific Leaf Area, Are Consistent Indicators Of Elevated Nutrient Inputs, Jennifer Firn, Kimberly J. La Pierre, Lori Biederman, Et Al. Jan 2019

Leaf Nutrients, Not Specific Leaf Area, Are Consistent Indicators Of Elevated Nutrient Inputs, Jennifer Firn, Kimberly J. La Pierre, Lori Biederman, Et Al.

Ecology, Evolution and Organismal Biology Publications

Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus and potassium concentrations increased in response to the addition of each respective soil nutrient. We found few significant changes in leaf traits when ...