PlanMine – a mineable resource of planarian biology and biodiversity

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.

SUMOylation controls stem cell proliferation and regional cell death through Hedgehog signaling in planarians

“…Components of the SUMOylation pathway were identified by BLASTing human SUMO protein sequences into available genomic resources for S. mediterranea [58,59]. Identified sequences underwent a six-frame translation using PFAM and conservation was further confirmed with UNI-PROT.…”

The NuRD complex componentp66suppresses photoreceptor neuron regeneration in planarians

“…Full length p66 mRNA was identified previously by RNA‐seq transcriptome assembly (dd_Smed_v6_3115_0_1, Planmine [Brandl et al. 2015], also found on SmedGD [Robb et al. 2015]).…”

Increased taxon sampling reveals thousands of hidden orthologs in flatworms

“…S2). However, OrthoFinder only recovered 82.7% (62/75) of the putative hidden orthologs identified by the single "bridge" Leapfrog pipeline in the same S. mediterranea transcriptome (Brandl et al 2016) with a similar E-value cutoff. Remarkably, the inclusion of the entire data set in OrthoFinder reduced the number of orthogroups shared by human and S. mediterranea (5213 orthogroups) and retrieved fewer putative hidden orthologs (56 of 75; 74.67%).…”

“…The use of more molecularly conserved flatworm lineages, such as P. vittatus, can improve the identification of candidate genes, as well as help with the annotation of the increasingly abundant flatworm RNA-seq and genomic data sets (Berriman et al 2009;Wang et al 2011;Tsai et al 2013;Robb et al 2015;Wasik et al 2015;Brandl et al 2016). Therefore, we have now made available an assembled version of those highly complete nonplanarian flatworm transcriptomes in PlanMine, an integrated web resource of transcriptomic data for planarian researchers (Brandl et al 2016). Importantly, the Leapfrog pipeline can also be exported to any set of transcriptomes/predicted proteins.…”