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PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity.

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Rozanski,  Andrei
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Moon,  HongKee
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Brandl,  Holger
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Grohme,  Markus
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Henry,  Ian
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Rink,  Jochen
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., et al. (2019). PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity. Nucleic acids research, 47(D1), 812-820. doi:10.1093/nar/gky1070.


Cite as: https://hdl.handle.net/21.11116/0000-0006-7E04-9
Abstract
Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of fascinating biology, including planarians with their astonishing regenerative abilities and the parasitic tape worms and blood flukes that exert a massive impact on human health. PlanMine (http://planmine.mpi-cbg.de/) has the mission objective of providing both a mineable sequence repository for planarians and also a resource for the comparative analysis of flatworm biology. While the original PlanMine release was entirely based on transcriptomes, the current release transitions to a more genomic perspective. Building on the recent availability of a high quality genome assembly of the planarian model species Schmidtea mediterranea, we provide a gene prediction set that now assign existing transcripts to defined genomic coordinates. The addition of recent single cell and bulk RNA-seq datasets greatly expands the available gene expression information. Further, we add transcriptomes from a broad range of other flatworms and provide a phylogeny-aware interface that makes evolutionary species comparisons accessible to non-experts. At its core, PlanMine continues to utilize the powerful InterMine framework and consistent data annotations to enable meaningful inter-species comparisons. Overall, PlanMine 3.0 thus provides a host of new features that makes the fascinating biology of flatworms accessible to the wider research community.