Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci
International audience Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen r...
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ftccsdartic:oai:HAL:hal-01768405v1 2023-05-15T15:49:57+02:00 Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci Martin, Jolyon Ponstingl, Hannes Lefranc, Marie-Paule Archer, Joy Sargan, David Bradley, Allan The Wellcome Trust Sanger Institute Cambridge Institut de génétique humaine (IGH) Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) University of Cambridge UK (CAM) 2018-04 https://hal.archives-ouvertes.fr/hal-01768405 https://doi.org/10.1007/s00251-017-1028-0 en eng HAL CCSD Springer Verlag info:eu-repo/semantics/altIdentifier/doi/10.1007/s00251-017-1028-0 info:eu-repo/semantics/altIdentifier/pmid/28924718 hal-01768405 https://hal.archives-ouvertes.fr/hal-01768405 doi:10.1007/s00251-017-1028-0 PUBMED: 28924718 ISSN: 0093-7711 EISSN: 1432-1211 Immunogenetics https://hal.archives-ouvertes.fr/hal-01768405 Immunogenetics, Springer Verlag, 2018, 70 (4), pp.223 - 236. ⟨10.1007/s00251-017-1028-0⟩ Antigen receptor Canine Immunoglobulin T cell receptor [SDV]Life Sciences [q-bio] [SDV.GEN]Life Sciences [q-bio]/Genetics info:eu-repo/semantics/article Journal articles 2018 ftccsdartic https://doi.org/10.1007/s00251-017-1028-0 2021-11-07T03:03:12Z International audience Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci. Article in Journal/Newspaper Canis lupus Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Lambda ENVELOPE(-62.983,-62.983,-64.300,-64.300) Immunogenetics 70 4 223 236 |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
Antigen receptor Canine Immunoglobulin T cell receptor [SDV]Life Sciences [q-bio] [SDV.GEN]Life Sciences [q-bio]/Genetics |
spellingShingle |
Antigen receptor Canine Immunoglobulin T cell receptor [SDV]Life Sciences [q-bio] [SDV.GEN]Life Sciences [q-bio]/Genetics Martin, Jolyon Ponstingl, Hannes Lefranc, Marie-Paule Archer, Joy Sargan, David Bradley, Allan Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci |
topic_facet |
Antigen receptor Canine Immunoglobulin T cell receptor [SDV]Life Sciences [q-bio] [SDV.GEN]Life Sciences [q-bio]/Genetics |
description |
International audience Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci. |
author2 |
The Wellcome Trust Sanger Institute Cambridge Institut de génétique humaine (IGH) Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) University of Cambridge UK (CAM) |
format |
Article in Journal/Newspaper |
author |
Martin, Jolyon Ponstingl, Hannes Lefranc, Marie-Paule Archer, Joy Sargan, David Bradley, Allan |
author_facet |
Martin, Jolyon Ponstingl, Hannes Lefranc, Marie-Paule Archer, Joy Sargan, David Bradley, Allan |
author_sort |
Martin, Jolyon |
title |
Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci |
title_short |
Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci |
title_full |
Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci |
title_fullStr |
Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci |
title_full_unstemmed |
Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci |
title_sort |
comprehensive annotation and evolutionary insights into the canine (canis lupus familiaris) antigen receptor loci |
publisher |
HAL CCSD |
publishDate |
2018 |
url |
https://hal.archives-ouvertes.fr/hal-01768405 https://doi.org/10.1007/s00251-017-1028-0 |
long_lat |
ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
geographic |
Lambda |
geographic_facet |
Lambda |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
ISSN: 0093-7711 EISSN: 1432-1211 Immunogenetics https://hal.archives-ouvertes.fr/hal-01768405 Immunogenetics, Springer Verlag, 2018, 70 (4), pp.223 - 236. ⟨10.1007/s00251-017-1028-0⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1007/s00251-017-1028-0 info:eu-repo/semantics/altIdentifier/pmid/28924718 hal-01768405 https://hal.archives-ouvertes.fr/hal-01768405 doi:10.1007/s00251-017-1028-0 PUBMED: 28924718 |
op_doi |
https://doi.org/10.1007/s00251-017-1028-0 |
container_title |
Immunogenetics |
container_volume |
70 |
container_issue |
4 |
container_start_page |
223 |
op_container_end_page |
236 |
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1766384958419501056 |