Apr 28, 2016

Increased taxon sampling reveals thousands of hidden orthologs in flatworms

BioRxiv : the Preprint Server for Biology
Jose M Martin-DuranAndreas Hejnol

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 complement of an organism consists of hidden orthologs, those with no apparent homology with common 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 hidden orthologs in large transcriptomic databases. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3,427 hidden orthologs, some of them not identified by OrthoFinder, a common orthogroup inference algorithm. Unexpectedly, we do not observe a correlation between the number of hidden orthologs in a lineage and its "average" evolutionary rate. Hidden orthologs do not show unusual sequence composition biases (e.g. GC content, average length, domain composition) that might account for systematic errors in sequence ...Continue Reading

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Mentioned in this Paper

Homeo Domain
Genome
Genes
Basic Local Alignment Search Tool
Centrosome
Genomics
Organism
Platyhelminthes
Gene Duplication Abnormality
Paralogous Gene

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