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

Andrei Rozanski, HongKee Moon, Holger Brandl, José M Martín-Durán, Markus A Grohme, Katja Hüttner, Kerstin Bartscherer, Ian Henry, Jochen C Rink

Research output: Contribution to journal/periodicalArticleScientificpeer-review

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.

Original languageEnglish
Pages (from-to)D812-D820
JournalNucleic Acids Research
Volume47
Issue numberD1
DOIs
Publication statusPublished - 08 Jan 2019
Externally publishedYes

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