Biosciences News

A pan-genome, the non-redundant union of all the sets of genes found in individuals of a species, is a valuable resource for unlocking natural diversity. However, the computational resources required to produce a large number of high quality genome assemblies has been a limiting factor in creating plant pan-genomes. In Nature Communications, an international team led by JGI researchers gauged the size of a plant pan-genome using the JGI Plant Flagship Genome of Brachypodium distachyon, a wild grass widely used as a model for grain and biomass crops. Read more on the JGI website.

To help improve crop breeding strategies and overcome challenges such as making plants more tolerant of marginal lands, and stresses such as drought and low nutrient availability, researchers are focusing on understanding and promoting beneficial plant-microbe relationships. In Nature Genetics, a team led by JGI and University of North Carolina at Chapel Hill researchers assembled a catalog of plant and microbial genomes to identify and characterize candidate genes that aid bacteria in adapting to plant environments. “Here we used a massive genomic and computational effort to address the fundamental and important question: ‘How does the plant microbiome interact with the plant?’” said study co-first author and JGI research scientist Asaf Levy, a research scientist at the JGI. Read more on the JGI website.

Neuroscientists can now explore a beta version of the new Neurodata Without Borders: Neurophysiology (NWB:N 2.0) software and offer input to its developers. The 2.0 software was developed by Berkeley Lab Computational Research Division’s (CRD’s) Oliver Ruebel and Andrew Tritt, in collaboration with Kristofer Bouchard (Biological Systems & Engineering Division, pictured), Loren Frank and Eddie Chang (UCSF), and the broader Neurodata Without Borders community. Read more on CRD’s website.

Jenny Mortimer, Deputy Vice President of the Feedstocks Division at the Joint BioEnergy Institute (JBEI) and Research Scientist with the Environmental Genomics and Systems Biology (EGSB) Division collaborated with a team of international researchers headed by scientists from the University of Tübingen to decipher the workings of the Cytolysin toxin, which is produced by some of the world’s most devastating crop diseases. The study shows that the Cytolysin binds to a class of glycosylated sphingolipid that Mortimer’s group studies. By producing plants which have modified forms of the sphingolipid, the toxin binding specificity could be determined. The study was published in Science today, December 14, and its findings may lead to ways of better protecting crops from such pathogens in the future. Read the Science news article about the study.

In heritable mutualisms, hosts pass on beneficial symbionts between generations. The origin of this relationship though, is often antagonistic and the parasite first needs to secure its own transmission before working with the host. Using the mutualistic relationship between the plant pathogenic fungus Rhizopus microsporus (Rm) and Burkholderia endobacteria, JGI and Cornell University researchers reported on how the antagonistic-to-mutualistic transition occurs in Nature Communications. The team found that the oil-producing fungus is highly dependent on the Burkholderia endobacteria to proliferate both sexually and asexually. This dependence is consistent with the addiction model of mutualism evolution. Read more on the JGI website.