CyVerse: Cyberinfrastructure for open science.

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles.

Plant traits and vegetation data from climate warming experiments along an 1100 m elevation gradient in Gongga Mountains, China.

Functional trait data enhance climate change research by linking climate change, biodiversity response, and ecosystem functioning, and by enabling comparison between systems sharing few taxa. Across four sites along a 3000-4130 m a.s.

Dual Utilization of Medicinal and Aromatic Crops as Bioenergy Feedstocks.

Dual production of biofuels and chemicals can increase the economic value of lignocellulosic bioenergy feedstocks. We compared the bioenergy potential of several essential oil (EO) crops with switchgrass ( Panicum virgatum L.), a crop chosen to benchmark biomass and lignocellulosic biofuel production.

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms.

This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative transcriptomics. It also serves as a primer for biologists to develop data scientist computational skills, e.g.

FractBias: a graphical tool for assessing fractionation bias following polyploidy.

Summary: Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns.

Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology.

High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the "Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology" symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans.

Effects of Produced Water on Soil Characteristics, Plant Biomass, and Secondary Metabolites.

The Powder River Basin in Wyoming and Montana contains the United States' largest coal reserve. The area produces large amounts of natural gas through extraction from water-saturated coalbeds. Determining the impacts of coalbed natural gas-produced efflux water on crops is important when considering its potential use as supplemental irrigation water.

Ethanol and High-Value Terpene Co-Production from Lignocellulosic Biomass of Cymbopogon flexuosus and Cymbopogon martinii.

Cymbopogon flexuosus, lemongrass, and C. martinii, palmarosa, are perennial grasses grown to produce essential oils for the fragrance industry. The objectives of this study were (1) to evaluate biomass and oil yields as a function of nitrogen and sulfur fertilization, and (2) to characterize their utility for lignocellulosic ethanol compared to Panicum virgatum (switchgrass).

Ketocarotenoid Production in Soybean Seeds through Metabolic Engineering.

The pink or red ketocarotenoids, canthaxanthin and astaxanthin, are used as feed additives in the poultry and aquaculture industries as a source of egg yolk and flesh pigmentation, as farmed animals do not have access to the carotenoid sources of their wild counterparts. Because soybean is already an important component in animal feed, production of these carotenoids in soybean could be a cost-effective means of delivery. In order to characterize the ability of soybean seed to produce carotenoids, soybean cv.

Morphology and ploidy level determination of Pteris vittata callus during induction and regeneration.

Background: Morphological and ploidy changes of the arsenic hyperaccumulator, Chinese brake fern (Pteris vittata) callus tissue are described here to provide insight into fern life cycle biology and for possible biotechnology applications. Pteris vittata callus was studied using transmission and scanning electron microscopy, and flow cytometry.

Results: Callus induction occurred both in light and dark culture conditions from prothallus tissues, whereas rhizoid formation occurred only in dark culture conditions.

Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes.

Unresolved questions about evolution of the large and diverse legume family include the timing of polyploidy (whole-genome duplication; WGDs) relative to the origin of the major lineages within the Fabaceae and to the origin of symbiotic nitrogen fixation. Previous work has established that a WGD affects most lineages in the Papilionoideae and occurred sometime after the divergence of the papilionoid and mimosoid clades, but the exact timing has been unknown. The history of WGD has also not been established for legume lineages outside the Papilionoideae.

Stable transformation of ferns using spores as targets: Pteris vittata and Ceratopteris thalictroides.

Ferns (Pteridophyta) are very important members of the plant kingdom that lag behind other taxa with regards to our understanding of their genetics, genomics, and molecular biology. We report here, to our knowledge, the first instance of stable transformation of fern with recovery of transgenic sporophytes. Spores of the arsenic hyperaccumulating fern Pteris vittata and tetraploid 'C-fern Express' (Ceratopteris thalictroides) were stably transformed by Agrobacterium tumefaciens with constructs containing the P.

Switchgrass (Panicum virgatum L.) cell suspension cultures: Establishment, characterization, and application.

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that has received considerable attention as a potential dedicated biofuel and bioproduct feedstock. Genetic improvement of switchgrass is needed for better cellulosic ethanol production, especially to improve cellulose-to-lignin ratios.

Switchgrass (Panicum virgatum L.) polyubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation.

Background: The ubiquitin protein is present in all eukaryotic cells and promoters from ubiquitin genes are good candidates to regulate the constitutive expression of transgenes in plants. Therefore, two switchgrass (Panicum virgatum L.) ubiquitin genes (PvUbi1 and PvUbi2) were cloned and characterized.

Elevational and seasonal variation in the foliar quality and arthropod community of Acer pensylvanicum.

Elevational gradients provide natural experiments for examining how variation in abiotic forces such as nutrient mineralization rates, risk of photodamge, temperature, and precipitation influence plant-insect interactions. At the Coweeta LTER site in the Southern Appalachian Mountains, we examined spatial and temporal variation in striped maple, Acer pensylvanicum, foliar quality and associated patterns in the arthropod community. Variation in herbivore densities was associated more strongly with seasonal variation in plant quality than with spatial variation in quality among three sampling sites.

Within-plant distribution and emission of sesquiterpenes from Copaifera officinalis.

Copaifera officinalis, the diesel tree, is known for massive production of oleoresin, mainly composed of sesquiterpene hydrocarbons. In this study, composition of these sesquiterpenes and their concentrations in leaves, stems and roots of C. officinalis at two developmental stages, including the three-week old (TW) seedlings and two-year old (TY) trees, were determined.