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Barnes IHA, Ibarra-Soria X, Fitzgerald S, Gonzalez JM, Davidson C, Hardy MP, Manthravadi D, Van Gerven L, Jorissen M, Zeng Z, Khan M, Mombaerts P, Harrow J, Logan DW, Frankish A. Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons. BMC Genomics 2020; 21:196. [PMID: 32126975 PMCID: PMC7055050 DOI: 10.1186/s12864-020-6583-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND 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. RESULTS 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. CONCLUSIONS 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.
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Affiliation(s)
- If H A Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Stephen Fitzgerald
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jose M Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Matthew P Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Laura Van Gerven
- Department of ENT-HNS, UZ Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Mark Jorissen
- Department of ENT-HNS, UZ Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Zhen Zeng
- Max Planck Research Unit for Neurogenetics, Max von-Laue-Strasse 4, 60438, Frankfurt, Germany
| | - Mona Khan
- Max Planck Research Unit for Neurogenetics, Max von-Laue-Strasse 4, 60438, Frankfurt, Germany
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Max von-Laue-Strasse 4, 60438, Frankfurt, Germany
| | - Jennifer Harrow
- ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Darren W Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Monell Chemical Senses Center, Philadelphia, PA, 19104, USA
- Waltham Petcare Science Institute, Leicestershire, LE14 4RT, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IHA, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012; 335:823-8. [PMID: 22344438 PMCID: PMC3299548 DOI: 10.1126/science.1215040] [Citation(s) in RCA: 869] [Impact Index Per Article: 72.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease-causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.
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Abstract
Tunisia is a medium-level epidemic country for hepatitis B virus (HBV). This study characterizes, for the first time, full genome HBV strains from Tunisia. Viral load quantification and phylogenetic analyses of full genome or pre-S/S sequences were performed on 196 hepatitis B surface antigen (HBsAg)-positive plasma samples from Tunisian blood donors. The median viral load was 64.65 IU ml(-1) (range<5-7.7x10(8) IU ml(-1)) and 89% of samples had viral loads below 10,000 IU ml(-1). Fifty-nine strains formed a novel subgenotype D7, 41 strains clustered in subgenotype D1, seven strains in subgenotype A2 and one strain in genotype C. The novel subgenotype D7 was defined by maximum Bayesian posterior probability, a genetic divergence from other HBV/D subgenotypes by >4% and a stronger HBV/E signal in the X to core genes than subgenotype D1. In conclusion, HBV/D is dominant in asymptomatic Tunisian HBsAg carriers and a novel subgenotype, D7, was the most common subgenotype found in this population.
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Affiliation(s)
- Birgit H M Meldal
- Division of Transfusion Medicine, Department of Haematology, University of Cambridge, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | | | - If H A Barnes
- Division of Transfusion Medicine, Department of Haematology, University of Cambridge, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
| | | | - Jean-Pierre Allain
- Division of Transfusion Medicine, Department of Haematology, University of Cambridge, Cambridge Blood Centre, Long Road, Cambridge CB2 0PT, UK
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