PhycoCosm, a comparative algal genomics resource

Abstract

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.

Figure 1.

PhycoCosm Navigator with the Bacillariophyta leaf node clicked to show the drop down menu with a list of sequenced genomes, publication status (green if genome has been published), annotation and analysis tools, and the menu header ‘Bacillariophyta’ linking to the corresponding PhyloGroup.

Figure 2.

(A) The PhycoCosm genome browser view of the Chlamydomonas reinhardtii DGTT1 locus shows an acyltransferase involved in triacylglycerol accumulation and induced by nitrogen (N) starvation. Visible tracks are a sample of those possible. The GeneCatalog track shows the DGTT1 gene (right side) and a downstream cell cycle gene model (left side). The two RNAseq tracks 0 and 8 h after N starvation show that DGTT1 is induced while the cell cycle gene is not (9). The ChIPseq and 6mA tracks show H3K4me3 histone and N⁶-deoxymethyladenine (6mA) DNA modifications, respectively, at the 5′ end of DGTT1. The light and dark 6mA tracks suggest light regulation (10). The SNPs track displays polymorphisms found by resequencing 39 strains (11). The Peptides track from a cell cycle proteomics study supports the cell cycle gene model (12). (B) The protein page for the C. reinhardtii DGTT1 locus shows an expressed multi-exonic gene (CDS in red, UTR regions in blue, and translation in green) that encodes a membrane-anchored acyltransferase, as determined by automated annotation (secretion signal prediction in blue, predicted domain in orange, and BLAST alignments in gray) and manual curation (user annotation). The protein page links back to the genome browser (A) and a corresponding Phytozome page.

Figure 3.

Circular representation of the Guillardia theta plastid genome. Gene models are along the outside of the ring and colored according to the legend. The inner line graph represents average %GC across the genome, ranging (inner to outer) from 0 to 100%. Using the dropdown menu on the navigation toolbar, users are also able to view the mitochondrial and nucleomorph genomes (6). Genomes are plotted using Circos (16).

Figure 4.

The PhycoCosm comparative tools. (A) The Tree tab for the Bacillariophyta PhyloGroup illustrates the classical division of diatoms between Coscinodiscophyceae and Bacillariophyceae (17). (B) The Annotation tab's Transcription Factors feature for the Bacillariophyta PhyloGroup shows that the abundance of transcription factors with MYND finger domains is highly variable among diatoms (18). (C) KEGG maps shows annotation of EC 2.1.1.14, cobalamin-independent methionine synthase, for C. reinhardtii (on top, box colored red), but not for Volvox carteri (on bottom, box colored black), consistent with the experimental observation of vitamin B12 auxotrophy in V. carteri but not in C. reinhardtii (19,20). (D) The MCL Clusters tab confirms that the cobalamin-dependent methionine synthase gene family is shared by both C. reinhardtii and V. carteri, but V. carteri does not possess the cobalamin-independent methionine synthase, thus complementing the KEGG pathway analysis feature (C). (E) The Synteny tab's dotplot visualizes high synteny between two Ostreococcus genomes with some genome reshuffling between chromosomes 2 of both species and the higher numbered chromosomes (21).