News

A decade after the complete representative genomes of three Ostreococcus groups were sequenced, an international team of researchers including scientists at the Department of Energy Joint Genome Institute (DOE JGI) have resequenced and analyzed the genomes of 13 members of a natural population from the northwest Mediterranean Sea. The analysis revealed that the O. tauri population is larger than anticipated, with high genetic and phenotypic diversity that is influenced by the algae’s natural resistance to ocean viruses. Understanding the genetic variability of various Ostreococcus strains will help researchers understand how environmental changes affect their abundance and ability to photosynthesize. The work was reported in Science Advances. Read more in this DOE JGI Science Highlight.

Using a genetic mouse model developed at Berkeley Lab with CRISPR/Cas9 editing technology, University of California, Davis, researchers led by Alexander Nord have examined the developmental impact of a specific mutation found in some rare cases of autism spectrum disorder (ASD). The project began while Nord—now an assistant professor with the Center for Neuroscience at UC Davis—was a postdoc in the Mammalian Functional Genomics Laboratory of Berkeley Lab co-authors Axel Visel, Len Pennacchio, and Diane Dickel. In a paper published June 26 in the journal Nature Neuroscience, the researchers report that mice with a loss-of-function mutation in one copy of the CHD8 gene have increased brain volume and cognitive impairment, similar to that seen in people with the same mutation. CHD8 encodes a protein responsible for packaging DNA in cells, which in turn controls gene expression during development. Read more from UC Davis.

Department of Energy Joint Genome Institute (DOE JGI) and Biosciences Environmental Genomics and Systems Biology (EGSB) division researchers have released 1,003 reference genomes for diverse bacteria and archea isolated from environments ranging from sea water and soil, to plants, and to cow rumen and termite guts. The release is the largest to date from JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, which seeks to fill in unexplored branches of the tree of microbial life. JGI’s Supratim Mukherjee and Rekha Seshadri were co-first authors on the paper published in Nature Biotechnology; senior author Nikos Kyrpides and co-authors Natalia Ivanova, Axel Visel, Tanja Woyke, and Yasuo Yoshikuni have secondary affiliations with EGSB. The genomes are publicly available through the Integrated Microbial Genomes with Microbiomes (IMG/M) system. Read more on the JGI website.

Fungi, particularly those found in the digestive tracts of ruminant herbivores such as cattle, sheep, and goats, are very good at overcoming the resistance of plant cell walls to degradation—a major hurdle in the quest to produce sustainable fuels and chemicals from bioenergy feedstocks. Now, an international group of researchers has identified protein scaffolds in anaerobic gut fungi that provide docking sites for various enzymes, keeping them in place so that they can work together more effectively. As reported in the May 26 issue of Nature Microbiology, the structures are analogous to cellulosome complexes in anerobic bacteria, but this is the first time they have been found in fungi.

Scientists have sequenced the genome of a green alga that has drawn commercial interest as a strong producer of quality lipids for biofuel production. The chromosome-assembly genome of Chromochloris zofingiensis provides a blueprint for new discoveries in sustainable biofuels, antioxidants, and other valuable bioproducts. The team was led by Kris Niyogi, faculty biologist in the Molecular Biophysics and Integrated Bioimaging Division and included researchers from UCLA and UCSF. The alga was imaged in the National Center for X-ray Tomography, located at the Advanced Light Source. Read the science short at the Berkeley Lab News Center.