De Novo , Divergence, and Mixed Origin Contribute to the Emergence of Orphan Genes in Pristionchus Nematodes

• Published in: G3 : genes - genomes - genetics Vol. 9; no. 7; pp. 2277 - 2286
• Main Authors: Prabh, Neel, Rödelsperger, Christian
• Format: Journal Article
• Language: English
• Published: England Genetics Society of America 01.07.2019; Oxford University Press
• Subjects: Amino Acid Sequence; Animals; annotation artifacts; Computational Biology - methods; de novo genes; frame-shift; Genes, Protozoan; Genome, Protozoan; Genomics - methods; Investigations; Molecular Sequence Annotation; Orphan genes; Reading Frames; Reproducibility of Results; Rhabditida - classification; Rhabditida - genetics; Species Specificity; taxonomically-restricted; Orphan genes; frame-shift; de novo genes; annotation artifacts; taxonomically-restricted
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1534/g3.119.400326

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 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 exons. In addition, we present two cases of complete origination from non-coding regions, which represents one of the first reports of genes in nematodes. Thus, we conclude that emergence, divergence, and mixed mechanisms contribute to novel gene formation in nematodes.