One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012

Abstract

dictyBase (http://dictybase.org), the model organism database for Dictyostelium discoideum, includes the complete genome sequence and expression data for this organism. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. dictyBase has recently expanded to include the genome sequences of three additional Dictyostelids and has added new software tools to facilitate multigenome comparisons. The Dicty Stock Center, a strain and plasmid repository for Dictyostelium research, has relocated to Northwestern University in 2009. This allowed us integrating all Dictyostelium resources to better serve the research community. In this chapter, we will describe how to navigate the Web site and highlight some of our newer improvements.

Fig. 1

Graphical gene display and curator statements on the Gene Page. The image (A) also serves as a link to the Genome Browser and depicts a gene in the ‘Watson’ direction (arrow pointing to the right) with the chromosomal coordinates on top. The thinner gene track on top is labeled with the gene ID (DDB_G…), whereas the curated model track is labeled with the sequence ID (DDB…). (B) Below the image, optional curator notes are displayed, in this example alerting the user that ESTs indicate an intron in the 5’ UTR of the gene. In (C), the DDB ID of the curated model links to a separate tab for the sequence page. Next to the ID is a green check mark indicating that a curator has reviewed the gene. Below, notes describe where the curated model is derived from and what evidence supports the curated model.

Fig. 2

Community annotation display on the Gene Page. When a community annotation has been added to the wiki page for the gene, curators add a summary of that annotation in the description field, followed by the name of the submitter, date of annotation, and a link noting that there is more information on the wiki page (A). Curators also add a bold red link ‘View annotation for [gene name]’ (B). To the right of this link are more links to the wiki that you can find on each gene page: ‘Add an annotation for [gene name]’ and ‘Community Annotations Help’.

Fig. 3

The dictyBase Gene Page. (A) Tabbed browsing. The tabs on top link to Detail Pages as depicted in Fig. 4. (B) Page Navigation tools and link to Help. (C) General Information including gene names and product. (D) Genomic Information with coordinates and a map that links to Genome Browser. (E) Gene Product and gene model Information. (F) Links to sequences and BLAST server. (G) Associated Sequences. (H) Gene Ontology annotations. (I) Strain and Phenotype information. (J) External Links. (K) Gene Summary and (L) curation status note. (M) Latest References with links to paper details and PubMed.

Fig. 4

dictyBase Details Pages accessible from tabs on the Gene Page. (A) Protein Information including protein domains and sequence. (B) Complete Gene Ontology Info. (C) List of Orthologs. (D) Complete gene-related Strain and Phenotype info. (E). Complete list of References.

Fig. 5

The GBrowse Display. A view of 20 kb sequence on D. purpureum scaffold 12, coordinates 98,644 – 118,643. Note that the overview for this organism contains the genes present on the scaffold (E; see also Subheading 5.2). Tracks selected are: H, Genes; I, Gene Predictions from JGI; J, EST Alignments; and K, D. discoideum protein alignments. The view depicts 6 genes, one (DPU_G0052772) on the Watson strand (arrow head to the right) and the other genes on the Crick strand (arrow heads to the left). Three genes have EST alignments, and all genes have at least one D. discoideum protein aligned. Note the small ruler on top of the Details region (G); it can be expanded and moved to any desired location on the genomic stretch to check alignments. L shows an expansion of the available track options. From left to right, the functions are as follows: a add track to favorites; b, show or hide this track; c, turn off the track (may be activated again in track selection panel); d, share or export this track to another Gbrowse instance; e, configure the appearance of this track; f, download this track (Fasta, GFF3, GenBank); g, about this track.

Fig. 6

A. RNAseq tracks of different developmental time points displayed in Gbrowse. On top are the gene track and gene prediction (1) followed by the RNAseq developmental time points with a 4 hour interval, displayed chronologically from top down: 2, 0 hrs; 3, 4 hrs; 4, 8 hours; 5, 12 hrs; 6, 16 hrs; 7, 20 hrs; 8, 24 hrs. This is followed by two tracks that are “RNAseq 48 hrs prestalk” (9) and “RNAseq 48 hrs prespore” (10), where slugs were allowed to migrate for 48 hours before separating the cell types. The final track (11) contains all time points compiled into a single track. This gene, DPU_G0057736, the ortholog of D. discoideum calA, show increasing expression early in development (3) and a drop after 16 hrs (7); expression is higher in prestalk (9) than in prespore (10) cells. B. The GBrowse decorated FastA file. On the left (1) the decoration of this file is as follows: Yellow highlight: curated model; pink letters: Overlapping Sequencing Center and Geneid gene predictions; underline: ESTs. To the right (2) is an overview with the gene track and the curated gene model on top. Both gene predictions (3) are below, followed by ESTs (collapsed into one line), and RNAseq (all time points) aligned at the bottom. Note that the first exon of both gene predictions is much further upstream than the correct very short first exon (bases AT of the start codon) supported by ESTs and RNAseq. Start sites of gene predictions, curated model and supporting sequences are indicated by arrowheads.

Fig. 7

Strain Details Pages. As for all Stock Center pages, all strain records also have a shopping cart icon in the upper right corner making browsing of strains easy while the shopping cart can be accessed from everywhere. (A) A strain page of a wild type strain that is available at the Stock Center. Note the ‘Add to Cart’ and ‘Check Out’ buttons at the bottom. (B) Details of a mutant strain with one phenotype associated, but not yet available with a note in red above the strain record stating “This strain is not available at the Dicty Stock Center”.

Fig. 8

Strain Selection from Phenotype List on Gene Page and Shopping Cart Content. (A) A strain can be added to the shopping cart directly from the list of phenotypes on the Gene Page Tab (see also Fig. 4D). At the left of each strain/phenotype is either a green shopping cart when available (bottom strain), or a crossed-out gray cart when unavailable (top strain). (B) The Shopping Cart lists all items added to the cart with an option to remove it. When finished selecting click the ‘Check Out’ button at the bottom.