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Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?

Neel Prabh1, Christian Rödelsperger2

  • 1Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany.

BMC Bioinformatics
|June 2, 2016
PubMed
Summary
This summary is machine-generated.

Most orphan genes in Pristionchus pacificus are protein-coding genes, not artifacts or non-coding RNAs. This study validates their function using genomic, transcriptomic, and proteomic data, offering a transferable method for other species.

Keywords:
Gene expressionNegative selectionNematodesOrphan genesOrthologParalogdN/dS

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Genome sequencing reveals numerous orphan genes with unknown function.
  • Distinguishing functional orphan genes from genomic artifacts or non-coding RNAs is challenging.

Purpose of the Study:

  • To determine the nature of orphan genes in the nematode Pristionchus pacificus.
  • To ascertain if orphan genes are protein-coding or non-coding entities.

Main Methods:

  • Utilized genomic, transcriptomic, and proteomic data from P. pacificus.
  • Applied criteria: transcription indicates a biological entity; proteome data or negative selection indicates a protein-coding gene.
  • Validated gene structures experimentally for cases with evolutionary constraint but no expression data.

Main Results:

  • Between 42-81% of predicted orphan genes are expressed.
  • 39-76% of orphan genes show evidence of negative selection, indicating protein-coding function.
  • Experimental validation confirmed predicted gene structures for three constrained orphan genes.
  • Closely related genomes significantly improve the identification of negative selection in orphan genes.

Conclusions:

  • The majority of identified orphan genes in P. pacificus are confirmed as protein-coding genes.
  • The developed approach is applicable to other non-model organisms for orphan gene characterization.