@article {1899,
	title = {PlanMine 3.0{\textemdash}improvements to a mineable resource of flatworm biology and biodiversity},
	journal = {Nucleic Acids Researchnar},
	volume = {47},
	year = {2018},
	month = {2018},
	pages = {D812 - D820},
	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.},
	isbn = {0305-1048},
	url = {https://doi.org/10.1093/nar/gky1070},
	author = {Rozanski, Andrei and Brandl, Holger and Moon, HongKee and Grohme, Markus A and Henry, Ian and Rink, Jochen C and Martin-Duran, Jose M and H{\"u}ttner, Katja and Bartscherer, Kerstin}
}
@article {1740,
	title = {Increased taxon sampling reveals thousands of hidden orthologs in flatworms},
	journal = {Genome Res},
	year = {2017},
	month = {2017 Apr 11},
	abstract = {<p>Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages - mistakenly considered new genes - but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3,427 putative hidden orthologs, some of them not identified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its \&$\#$39;average\&$\#$39; evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g. planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution.</p>
},
	issn = {1549-5469},
	doi = {10.1101/gr.216226.116},
	author = {Martin-Duran, Jose M and Ryan, Joseph F and Vellutini, Bruno and Pang, Kevin and Hejnol, Andreas}
}
