Data from: Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

For genome assembly of C. zofingiensis strain SAG 211–14, we used a hybrid approach blending short reads (Illumina), long reads (Pacific Biosciences of California), and whole-genome optical mapping (OpGen) (SI Appendix, SI Text and Datasets S1–S19, and refer to SI Appendix, Datasets Key). The combined power of these approaches yielded a high-quality haploid nuclear genome of C. zofingiensis of ∼58 Mbp distributed over 19 chromosomes (Fig. 2) in the tradition of model organism projects, as opposed to the fragmentary “gene-space” assemblies typical of modern projects using high-throughput methods and associated software. Approximately 99% of reads from the Illumina genomic libraries were accounted for, and nonplaceholder chromosomal sequence covers ∼94% of the optical map. Because no automated pipeline was found able to achieve the desired quality, methods are described in SI Appendix, SI Text.

Genomics and Genetics

Agricultural Land Management Alternative with Numerical Assessment Criteria (ALMANAC) Simulation Model

The Agricultural Land Management Alternative with Numerical Assessment Criteria (ALMANAC) model simulates crop growth, competition, light interception by leaves, biomass accumulation, partitioning of biomass into grain, water use, nutrient uptake, and growth constraints such as water, temperature, and nutrient stress. Plant development is temperature driven, with duration of growth stages dependent on degree days. Each plant species has a defined base temperature and optimum temperature.

Agroecosystems & Environment

Data from: Shoot transcriptome of the giant reed, Arundo donax

The giant reed, Arundo donax, is a perennial grass species that has become an invasive plant in many countries. To establish a foundational molecular dataset, an llumina Hi-Seq protocol was used to sequence the transcriptome of actively growing shoots from an invasive genotype collected along the Rio Grande River, bordering Texas and Mexico. The assembly of 27,491 high confidence transcripts (≥200 bp) are reported with at least 70% coverage of known genes in other Poaceae species.

Plants and Crops

Eddy Covariance Data from Office of Naval Research Biofuel project on Maui

These data come from three eddy covariance (EC) towers that were installed as part of a project to assess the productivity of sugarcane agricultural systems for biofuel production. These towers were operated from 2011-2013 in Maui, USA. Major observational parameters include net carbon exchange, evapotranspiration, and energy fluxes.

Eddy Covariance tower establishment in Maui

Data from: Comparative farm-gate life cycle assessment of oilseed feedstocks in the Northern Great plains

This MS Word document contains the oilseed feedstock farm-gate model inventories, results, and uncertainty analyses for the Northern Great Plains discussed in Moeller et. al 2017. Analysis was conducted using IPCC GHG standardized emissions. Methodology is detailed in the associated publication (doi: 10.1007/s41247-017-0030-3). The supplementary information contains the names of the ecoinvent inventories; oilseed yield, seeding rates, and fertilization rates per USDA crop management zone (CMZ); climate change, freshwater eutrophication, and marine eutrophication percent contributions ReCiPe results per CMZ; Monte Carlo uncertainty results per CMZ; and farm-gate energy balance analysis results per CMZ.

Switchgrass ESTs and SNPs

As part of our project, “Developing Association Mapping in Polyploid Perennial Biofuel Grasses” (DOE-USDA Plant Feedstock Genomics for Bioenergy Program grant DE-A102-07ER64454)*, two SNP discovery initiatives were carried out. The earlier one (2009) was an approach based on EST sequences. The latest initiative (2011-12) adopted a more powerful approach, based on GBS (Genotyping by Sequencing). We believe that the SNP markers identified in these studies will greatly enhance breeding efforts that target the improvement of key biofuel traits and the development of new switchgrass cultivars.

Genomics and Genetics

Unit process data for bio-jet fuel production from poplar biomass via bioconversion at a biorefinery

A partial Life Cycle Assessment (LCA) is conducted to investigate the life cycle impacts of a biorefinery designed to convert poplar tree chips into jet fuel via fermentation and subsequent hydrogenation. The goal of producing jet fuel from Populus (poplar) trees (bio-jet) is to create an alternative to petroleum based jet fuel (petro-jet). Currently no jet fuel producing biorefineries are in commercial operation and the results of this LCA will be used to assess a potential environmental impact that could result from scaling up the proposed system. Work is part of the Advanced Hardwood Biofuels Northwest project.

Life Cycle Assessment program