title: Increased taxon sampling reveals thousands of hidden orthologs in flatworms.
abstract: 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 3427 putative hidden orthologs, some unidentified 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 "average" 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.
authors.affiliation: Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway.
authors.forename: José M
authors.identifier: 0000-0002-2572-1061
authors.initials: JM
authors.lastname: Martín-Durán
authors.affiliation: Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway.|Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA.
authors.forename: Joseph F
authors.identifier: 0000-0001-5478-0522
authors.initials: JF
authors.lastname: Ryan
authors.affiliation: Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway.
authors.forename: Bruno C
authors.identifier: 0000-0002-0000-9465
authors.initials: BC
authors.lastname: Vellutini
authors.affiliation: Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway.
authors.forename: Kevin
authors.identifier: 0000-0002-2365-9022
authors.initials: K
authors.lastname: Pang
authors.affiliation: Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway.
authors.forename: Andreas
authors.identifier: 0000-0003-2196-8507
authors.initials: A
authors.lastname: Hejnol
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D017238:Genes, Helminth; D010986:Platyhelminths / Q000145:classification* / Q000235:genetics*; D059467:Transcriptome