title: 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.
authors.affiliation: Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.
authors.forename: Sofia M C
authors.initials: SM
authors.lastname: Robb
authors.affiliation: Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.
authors.forename: Kirsten
authors.initials: K
authors.lastname: Gotting
authors.affiliation: Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.
authors.forename: Eric
authors.initials: E
authors.lastname: Ross
authors.affiliation: Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sánchez Alvarado
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D016678:Genome; D015801:Helminth Proteins / Q000235:genetics; D020407:Internet; D058977:Molecular Sequence Annotation; D010932:Planarians / Q000235:genetics* / Q000378:metabolism; D012038:Regeneration / Q000235:genetics
chemical_list: D015801:Helminth Proteins
keywords: GBrowse; GMOD; Schmidtea mediterranea; planaria genome