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  De Novo, divergence, and mixed origin contribute to the emergence of orphan genes in Pristionchus nematodes

Prabh, N., & Rödelsperger, C. (2019). De Novo, divergence, and mixed origin contribute to the emergence of orphan genes in Pristionchus nematodes. G3: Genes, Genomes, Genetics, 9(7), 2277-2286. doi:10.1534/g3.119.400326.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-BE55-7 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-1F4E-3
Genre: Journal Article

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Prabh, Neel1, Author              
Rödelsperger,, Christian, Author
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1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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 Abstract: Homology is a fundamental concept in comparative biology. It is extensively used at the sequence level to make phylogenetic hypotheses and functional inferences. Nonetheless, the majority of eukaryotic genomes contain large numbers of orphan genes lacking homologs in other taxa. Generally, the fraction of orphan genes is higher in genomically undersampled clades, and in the absence of closely related genomes any hypothesis about their origin and evolution remains untestable. Previously, we sequenced ten genomes with an underlying ladder-like phylogeny to establish a phylogenomic framework for studying genome evolution in diplogastrid nematodes. Here, we use this deeply sampled data set to understand the processes that generate orphan genes in our focal species Pristionchus pacificus. Based on phylostratigraphic analysis and additional bioinformatic filters, we obtained 29 high-confidence candidate genes for which mechanisms of orphan origin were proposed based on manual inspection. This revealed diverse mechanisms including annotation artifacts, chimeric origin, alternative reading frame usage, and gene splitting with subsequent gain of de novo exons. In addition, we present two cases of complete de novo origination from non-coding regions, which represents one of the first reports of de novo genes in nematodes. Thus, we conclude that de novo emergence, divergence, and mixed mechanisms contribute to novel gene formation in Pristionchus nematodes.

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Language(s): eng - English
 Dates: 2019-02-042019-05-112019-07-012019-07
 Publication Status: Published in print
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 Identifiers: DOI: 10.1534/g3.119.400326
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Title: G3: Genes, Genomes, Genetics
Source Genre: Journal
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Publ. Info: Bethesda : Genetics Society of America
Pages: - Volume / Issue: 9 (7) Sequence Number: - Start / End Page: 2277 - 2286 Identifier: Other: 2160-1836
Other: http://www.sherpa.ac.uk/romeo/issn/2160-1836/
CoNE: https://pure.mpg.de/cone/journals/resource/2160-1836