SmedGD 2.0: The Schmidtea mediterranea genome database

Abstract

Planarians have emerged as excellent models for the study of key biological processes such as stem cell function and regulation, axial polarity specification, regeneration, and tissue homeostasis among others. The most widely used organism for these studies is the free-living flatworm Schmidtea mediterranea. In 2007, the Schmidtea mediterranea Genome Database (SmedGD) was first released to provide a much needed resource for the small, but growing planarian community. SmedGD 1.0 has been a depository for genome sequence, a draft assembly, and related experimental data (e.g., RNAi phenotypes, in situ hybridization images, and differential gene expression results). We report here a comprehensive update to SmedGD (SmedGD 2.0) that aims to expand its role as an interactive community resource. The new database includes more recent, and up-to-date transcription data, provides tools that enhance interconnectivity between different genome assemblies and transcriptomes, including next-generation assemblies for both the sexual and asexual biotypes of S. mediterranea. SmedGD 2.0 (http://smedgd.stowers.org) not only provides significantly improved gene annotations, but also tools for data sharing, attributes that will help both the planarian and biomedical communities to more efficiently mine the genomics and transcriptomics of S. mediterranea.

Keywords: GBrowse; GMOD; Schmidtea mediterranea; planaria genome.

Figure 1

Smed Unigene page Panel a: In the Genome browser a pop-up balloon provides a link from each Smed Unigene alignment to the Smed Unigene Gene Page. Panel b: An example of a Smed Unigene “Gene page”. The header region contains a summary of the Smed Unigene which includes its identifier, SMU15012603 (links back to Smed Unigene Browser), the bioinformatically determined putative function, Histone Deacteylase 1, a count of the number of transcripts (4) from the number of libraries, or RNASeq experiments, (4) by which this Smed Unigene is represented. Panel c: Smed Unigene Gene Pages provide genome browser links to alignments for that Smed Unigene in each genome assembly. Panel d: An example of the web page for retrieving Amino Acid Sequence. Clicking on the button labeled ”Get AA Sequence” (green arrow in panel A) will provide the amino acid sequence of Smed Unigene. Clicking on the button labeled “get NT Sequence” (panel A) will provide the nucleotide sequences of the transcripts that were clustered to generate this Smed Unigene.

Figure 2

BLAST interface Panel a: BLAST form. The form allows for alignment to sequence databases available in SmedGD 2.0. Panel b: BLAST result table. When blasting to the Smed Unigenes database, BLAST results are formatted in a table with links to the Smed Unigenes GBrowse, the Smed Unigene Gene Page (green arrow), and to downloads of the amino acid (AA) and nucleotide sequences (NT). Panel c: An example of the genome browser displaying Smed Unigene BLAST results.

Figure 3

Smed Unigene Protein Search Page Panel a: Smed Unigene Protein Search. Protein motifs (coil-coiled, transmembrane, and/or signal peptides) can be selected and limited by adding additional search criteria such as protein descriptions, protein names, or amino acid length. A search with just text provided in the Search Protein Descriptions can be performed without any additional protein domains selected. Panel b: Smed Unigene Protein Search results page. The search returns a list of Smed Unigenes with their putative function and a link the Smed Unigene Gene Page.