Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

• Published in: BMC genomics Vol. 21; no. 1; p. 196
• Main Authors: Barnes, If H A, Ibarra-Soria, Ximena, Fitzgerald, Stephen, Gonzalez, Jose M, Davidson, Claire, Hardy, Matthew P, Manthravadi, Deepa, Van Gerven, Laura, Jorissen, Mark, Zeng, Zhen, Khan, Mona, Mombaerts, Peter, Harrow, Jennifer, Logan, Darren W, Frankish, Adam
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03-03-2020; BioMed Central; BMC
• Subjects: Animals; Annotation; Annotations; Conserved Sequence; Curation; Data Curation - methods; Databases, Genetic; DNA sequencing; Exons; Exons (Molecular genetics); Exons - genetics; Genes; Genetic aspects; Genetic Loci; Genome, Human; Genomes; Genomics; House mouse; Human; Humans; Loci; Mammals; Methods; Mice; Mouse; Non-coding RNA; Observations; Olfactory receptor gene; Olfactory receptors; Proteins; Pseudogenes; Quantitative Trait Loci; Receptors, Odorant - genetics; Vertebrates; United Kingdom; Human; Curation; Mouse; Annotation; Olfactory receptor gene
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-6583-3

Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences.
Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon.
This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.