Genenames.org: the HGNC resources in 2015

Gray, Kristian; Yates, Bethan; Seal, Ruth L.; Wright, Mathew W.; Bruford, Elspeth A.

doi:10.1093/nar/gku1071

Cited by 483 publications

(414 citation statements)

References 45 publications

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“…5). We propose that zebrafish abcb2 be renamed tap1 (SI Appendix, Table S7) to maintain consistency with nomenclature used for orthologous genes, such as in humans (86).…”

Section: Methodsmentioning

confidence: 99%

Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution

McConnell

Hernandez

Wcisel

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Antigen processing and presentation genes found within the MHC are among the most highly polymorphic genes of vertebrate genomes, providing populations with diverse immune responses to a wide array of pathogens. Here, we describe transcriptome, exome, and whole-genome sequencing of clonal zebrafish, uncovering the most extensive diversity within the antigen processing and presentation genes of any species yet examined. Our CG2 clonal zebrafish assembly provides genomic context within a remarkably divergent haplotype of the core MHC region on chromosome 19 for six expressed genes not found in the zebrafish reference genome: mhc1uga, proteasome-β 9b (psmb9b), psmb8f, and previously unknown genes psmb13b, tap2d, and tap2e. We identify ancient lineages for Psmb13 within a proteasome branch previously thought to be monomorphic and provide evidence of substantial lineage diversity within each of three major trifurcations of catalytic-type proteasome subunits in vertebrates: Psmb5/Psmb8/Psmb11, Psmb6/ Psmb9/Psmb12, and Psmb7/Psmb10/Psmb13. Strikingly, nearby tap2 and MHC class I genes also retain ancient sequence lineages, indicating that alternative lineages may have been preserved throughout the entire MHC pathway since early diversification of the adaptive immune system ∼500 Mya. Furthermore, polymorphisms within the three MHC pathway steps (antigen cleavage, transport, and presentation) are each predicted to alter peptide specificity. Lastly, comparative analysis shows that antigen processing gene diversity is far more extensive than previously realized (with ancient coelacanth psmb8 lineages, shark psmb13, and tap2t and psmb10 outside the teleost MHC), implying distinct immune functions and conserved roles in shaping MHC pathway evolution throughout vertebrates.comparative genomics | proteasome and TAP evolution | major histocompatibility | MHC class I pathway | CG2 clonal zebrafish

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“…5). We propose that zebrafish abcb2 be renamed tap1 (SI Appendix, Table S7) to maintain consistency with nomenclature used for orthologous genes, such as in humans (86).…”

Section: Methodsmentioning

confidence: 99%

Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution

McConnell

Hernandez

Wcisel

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…To represent gene‐to‐phenotype associations, a submap was created for each gene, displaying all phenotypes associated with any given gene defect. Also incorporated at this stage are links to external databases (eg, Uniprot17 and HGNC18) and modes of inheritance. This approach enables a modular overview of the map, avoiding overwhelming the user with the “hairball” effect caused by the high connectivity of the network.…”

Section: Creation Of the Leigh Mapmentioning

confidence: 99%

Leigh map: A novel computational diagnostic resource for mitochondrial disease

Rahman¹,

Noronha

Thiele

et al. 2017

Annals of Neurology

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“…Species IDs were extracted from National Center for Biotechnology Information (NCBI) (NCBI Resource Coordinators, 2017) Taxonomy browser. Names of human and mouse genes were updated according to the HUGO Gene Nomenclature Committee (HGNC) (Gray, Yates, Seal, Wright, & Bruford, 2015) and Mouse Genome Database (Blake et al., 2017) and others in accordance to NCBI gene nomenclature if available. Gene synonyms used in articles are written in brackets.…”

Section: Methodsmentioning

confidence: 99%

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

Hrovatin

Kunej

2017

Ecology and Evolution

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Erstwhile, sex was determined by observation, which is not always feasible. Nowadays, genetic methods are prevailing due to their accuracy, simplicity, low costs, and time‐efficiency. However, there is no comprehensive review enabling overview and development of the field. The studies are heterogeneous, lacking a standardized reporting strategy. Therefore, our aim was to collect genetic sexing assays for mammals and assemble them in a catalogue with unified terminology. Publications were extracted from online databases using key words such as sexing and molecular. The collected data were supplemented with species and gene IDs and the type of sex‐specific sequence variant (SSSV). We developed a catalogue and graphic presentation of diagnostic tests for molecular sex determination of mammals, based on 58 papers published from 2/1991 to 10/2016. The catalogue consists of five categories: species, genes, SSSVs, methods, and references. Based on the analysis of published literature, we propose minimal requirements for reporting, consisting of: species scientific name and ID, genetic sequence with name and ID, SSSV, methodology, genomic coordinates (e.g., restriction sites, SSSVs), amplification system, and description of detected amplicon and controls. The present study summarizes vast knowledge that has up to now been scattered across databases, representing the first step toward standardization regarding molecular sexing, enabling a better overview of existing tests and facilitating planned designs of novel tests. The project is ongoing; collecting additional publications, optimizing field development, and standardizing data presentation are needed.

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Genenames.org: the HGNC resources in 2015

Cited by 483 publications

References 45 publications

Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution

Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution

Leigh map: A novel computational diagnostic resource for mitochondrial disease

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

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