New Publications Citing SmedGD

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Dataset for a Dugesia japonica de novo transcriptome assembly, utilized for defining the voltage-gated like ion channel superfamily

Chan JD, Zhang D, Liu X, Zarowiecki MZ, Berriman M, Marchant JS Data Brief 2016 Dec;9:1044-1047 PMID: 27909700 Abstract This data article provides a transcriptomic resource for the free living

Neuronal sources of hedgehog modulate neurogenesis in the adult planarian brain

Currie KW, Molinaro AM, Pearson BJ Elife 2016 Nov;5 PMID: 27864883 Abstract The asexual freshwater planarian is a constitutive adult, whose central nervous system (CNS) is in a state of

Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea

Lakshmanan V, Bansal D, Kulkarni J, Poduval D, Krishna S, Sasidharan V, Anand P, Seshasayee A, Palakodeti D G3 (Bethesda) 2016 Oct;6(10):3035-3048 PMID: 27489207 Abstract In eukaryotes, 3′ untranslated regions

A functional genomics screen in planarians reveals regulators of whole-brain regeneration

Roberts-Galbraith RH, Brubacher JL, Newmark PA Elife 2016 Sep;5 PMID: 27612384 Abstract Planarians regenerate all body parts after injury, including the central nervous system (CNS). We capitalized on this distinctive

Temporal regulation of planarian eye regeneration

Deochand ME, Birkholz TR, Beane WS Regeneration (Oxf) 2016 Aug;3(4):209-221 PMID: 27800171 Abstract While tissue regeneration is typically studied using standard injury models, in nature injuries vary greatly in the

PlanMine–a mineable resource of planarian biology and biodiversity

Brandl H, Moon H, Vila-Farré M, Liu SY, Henry I, Rink JC

Nucleic Acids Res. 2016 Jan;44(D1):D764-73

PMID: 26578570

Abstract

Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history traits. PlanMine (http://planmine.mpi-cbg.de/) aims to accomplish two primary missions: First, to provide an easily accessible platform for sharing, comparing and value-added mining of planarian sequence data. Second, to catalyze the comparative analysis of the phenotypic diversity amongst planarian species. Currently, PlanMine houses transcriptomes independently assembled by our lab and community contributors. Detailed assembly/annotation statistics, a custom-developed BLAST viewer and easy export options enable comparisons at the contig and assembly level. Consistent annotation of all transcriptomes by an automated pipeline, the integration of published gene expression information and inter-relational query tools provide opportunities for mining planarian gene sequences and functions. For inter-species comparisons, we include transcriptomes of, so far, six planarian species, along with images, expert-curated information on their biology and pre-calculated cross-species sequence homologies. PlanMine is based on the popular InterMine system in order to make the rich biology of planarians accessible to the general life sciences research community.

Set1 and MLL1/2 Target Distinct Sets of Functionally Different Genomic Loci In Vivo

Duncan EM, Chitsazan AD, Seidel CW, Sánchez Alvarado A

Cell Rep 2015 Dec;13(12):2741-55

PMID: 26711341

Abstract

Histone H3 lysine 4 trimethylation (H3K4me3) is known to correlate with both active and poised genomic loci, yet many questions remain regarding its functional roles in vivo. We identify functional genomic targets of two H3K4 methyltransferases, Set1 and MLL1/2, in both the stem cells and differentiated tissue of the planarian flatworm Schmidtea mediterranea. We show that, despite their common substrate, these enzymes target distinct genomic loci in vivo, which are distinguishable by the pattern each enzyme leaves on the chromatin template, i.e., the breadth of the H3K4me3 peak. Whereas Set1 targets are largely associated with the maintenance of the stem cell population, MLL1/2 targets are specifically enriched for genes involved in ciliogenesis. These data not only confirm that chromatin regulation is fundamental to planarian stem cell function but also provide evidence for post-embryonic functional specificity of H3K4me3 methyltransferases in vivo.

Export SVG and PDF Images

We have added the ability to export SVG and PDF images from our genome browsers. Just find the region of the genome you like, click on the ‘File’ drop down menu, then ‘Export as…’, then ‘…editable SVG image’ or ‘…high-res PDF’.

Planmine Transcripts Aligned

Transcriptomes from PlanMine – a mineable resource of planarian biology and biodiversity are now aligned to SmedSxl_v3.1, SmedSxl_v4.0, SmedAxl_v1.1. Look for the Planmine section in the “Selection Tracks” tab on each genome assembly browser.

Brandl, H., Moon, H., Vila-Farré, M., Liu, S.-Y., Henry, I., & Rink, J. C., PlanMine – a mineable resource of planarian biology and biodiversity., Nucleic Acids Research, gkv1148. doi:10.1093/nar/gkv1148 (2015)

Fabulous New SmedGD Banner

We are very thankful to the M.C. Escher Company for allowing us to display ‘Flatworms’ on SmedGD. www.mcescher.com

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano

Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M

Proc. Natl. Acad. Sci. U.S.A. 2015 Oct;112(40):12462-7

PMID: 26392545

Abstract

The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50 = 222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.

Ergot Alkaloids (Re)generate New Leads as Antiparasitics

Chan JD, Agbedanu PN, Grab T, Zamanian M, Dosa PI, Day TA, Marchant JS

PLoS Negl Trop Dis 2015 Sep;9(9):e0004063

PMID: 26367744

Abstract

Praziquantel (PZQ) is a key therapy for treatment of parasitic flatworm infections of humans and livestock, but the mechanism of action of this drug is unresolved. Resolving PZQ-engaged targets and effectors is important for identifying new druggable pathways that may yield novel antiparasitic agents. Here we use functional, genetic and pharmacological approaches to reveal that serotonergic signals antagonize PZQ action in vivo. Exogenous 5-hydroxytryptamine (5-HT) rescued PZQ-evoked polarity and mobility defects in free-living planarian flatworms. In contrast, knockdown of a prevalently expressed planarian 5-HT receptor potentiated or phenocopied PZQ action in different functional assays. Subsequent screening of serotonergic ligands revealed that several ergot alkaloids possessed broad efficacy at modulating regenerative outcomes and the mobility of both free living and parasitic flatworms. Ergot alkaloids that phenocopied PZQ in regenerative assays to cause bipolar regeneration exhibited structural modifications consistent with serotonergic blockade. These data suggest that serotonergic activation blocks PZQ action in vivo, while serotonergic antagonists phenocopy PZQ action. Importantly these studies identify the ergot alkaloid scaffold as a promising structural framework for designing potent agents targeting parasitic bioaminergic G protein coupled receptors.

A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells

Koziol U, Radio S, Smircich P, Zarowiecki M, Fernández C, Brehm K

Genome Biol Evol 2015 Aug;7(8):2136-53

PMID: 26133390

Abstract

Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus. They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis, ta-TRIMs are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIMs into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes.

SmedGD 2.0: The Schmidtea mediterranea genome database

Robb SM, Gotting K, Ross E, Sánchez Alvarado A

Genesis 2015 Aug;53(8):535-46

PMID: 26138588

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.

MK4 Search Function Fixed

The MAKER search functionality has been repaired. Sorry for any inconvenience.