GLBRC Data Sets

Highlighted below are a variety of published studies that include data that might be of interest to the scientific community.

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization
Mccormick RF, Truong SK, Sreedasyam A, Jenkins J, Shu S, Sims D, Kennedy M, Amirebrahimi M, Weers BD, Mckinley B, Mattison A, Morishige DT, Grimwood J, Schmutz J, & Mullet JE (2017). The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. The Plant Journal 93:338–354.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes.

Correction of misassembled region in the version 1 sorghum reference genome assembly and integration of new sequence.
Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate
Ong RG, Higbee A, Bottoms S, Dickinson Q, Xie D, Smith SA, Serate J, Pohlmann E, Jones AD, Coon JJ, Sato TK, Sanford GR, Eilert D, Oates LG, Piotrowski JS, Bates DM, Cavalier D, & Zhang Y (2016). Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate. Biotechnology for Biofuels 9:237.

Interannual variability in precipitation, particularly drought, can affect lignocellulosic crop biomass yields and composition, and is expected to increase biofuel yield variability. However, the effect of precipitation on downstream fermentation processes has never been directly characterized.

Fermentation profiles for Zymomonas mobilis 2032 grown in corn stover and switchgrass hydrolysates from different harvest years.
Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae
Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, Mcilwain SJ, Ong IM, Breuer RJ, Narasimhan RA, Mcgee MA, Dickinson Q, Reau AL, Xie D, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, & Landick R (2016). Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLOS Genetics 12: e1006372

The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production of renewable bioenergy.

Fig 1. Mutations in ISU1, HOG1, GRE3 and IRA2 co-segregate with the evolved xylose metabolism phenotypes.
Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen
Schwalbach MS, Keating DH, Tremaine M, Marner WD, Zhang Y, Bothfeld W, Higbee A, Grass JA, Cotten C, Reed JL, Sousa LDC, Jin M, Balan V, Ellinger J, Dale B, Kiley PJ, & Landick R (2012). Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen. Applied and Environmental Microbiology 78:3442–3457.

The physiology of ethanologenic Escherichia coli grown anaerobically in alkali-pretreated plant hydrolysates is complex and not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pretreated by ammonia fiber expansion.

Global gene expression patterns of GLBRCE1