PhycoCosm, a comparative algal genomics resource

Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.

Building a custom high-throughput platform at the Joint Genome Institute for DNA construct design and assembly—present and future challenges

The rapid design and assembly of synthetic DNA constructs have become a crucial component of biological engineering projects via iterative design–build–test–learn cycles. In this perspective, we provide an overview of the workflows used to generate the thousands of constructs and libraries produced each year at the U.S. Department of Energy Joint Genome Institute. Particular attention is paid to describing pipelines, tools used, types of scientific projects enabled by the platform and challenges faced in further scaling output.

Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K2

Bacillus subtilis strain natto VK161 was selected for its high production of vitamin K2. Its genome was sequenced and annotated in the Department of Energy-Joint Genome Institute (DOE-JGI) annotation pipeline. It resulted in a chromosome of 4,073,396 bp, which is composed of 4,332 protein-coding genes, 23 rRNA genes, and 77 tRNA genes.

Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains

Type strains of species are one of the most valuable resources in microbiology. During the last decade, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) projects at the US Department of Energy Joint Genome Institute (JGI) and their collaborators have worked towards sequencing the genome of all the type strains of prokaryotic species. A new project GEBA VI extends these efforts to functional genomics, including pangenome and transcriptome sequencing and exometabolite analyses. As part of this project, investigators with interests in specific groups of prokaryotes are invited to submit samples for analysis at JGI.

Phytophthora Genomics: The Plant Destroyers' Genome Decoded

The year 2004 was an exciting one for the Phytophthora research community. The United States Department of Energy Joint Genome Institute (JGI) completed the draft genome sequence of two Phytophthora species, Phytophthora sojae and Phytophthora ramorum. In August of that year over 50 people gathered at JGI in Walnut Creek, California, for an annotation jamboree and searched for the secrets and surprises that the two genomes have in petto. This culminated in a paper in Science in September of this year describing the highlights of the sequencing project and emphasizing the power of having the genome sequences of two closely related organisms. This MPMI Focus issue on Phytophthora genomics contains a number of more specialized manuscripts centered on gene annotation and genome organization, and complemented with manuscripts that rely on genomics resources.