02156nas a2200241   4500008004100000020001400041245009200055210007100147260000900218300001600227490000700243520143800250100002101688700001901709700001801728700002201746700001501768700002001783700002601803700002001829700002501849856004001874       2018                        eng d  a0305-104800aPlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity0 aPlanMine 30—improvements to a mineable resource of flatworm biol  c2018  aD812 - D8200 v473 aFlatworms (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.1 aRozanski, Andrei1 aBrandl, Holger1 aMoon, HongKee1 aGrohme, Markus, A1 aHenry, Ian1 aRink, Jochen, C1 aMartin-Duran, Jose, M1 aHüttner, Katja1 aBartscherer, Kerstin  uhttps://doi.org/10.1093/nar/gky107002351nas a2200169   4500008004100000022001400041245008000055210006900135260001600204520180600220100002602026700002002052700002102072700001602093700002002109856005202129       2017                        eng d  a1549-546900aIncreased taxon sampling reveals thousands of hidden orthologs in flatworms0 aIncreased taxon sampling reveals thousands of hidden orthologs i  c2017 Apr 113 a<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>
1 aMartin-Duran, Jose, M1 aRyan, Joseph, F1 aVellutini, Bruno1 aPang, Kevin1 aHejnol, Andreas  uhttps://continenticola.myspecies.info/node/1740