Comparative genomics of the Leukocyte Receptor Complex in carnivores
BackgroundThe mammalian Leukocyte Receptor Complex (LRC) chromosomal region may contain gene families for the killer cell immunoglobulin-like receptor (KIR) and/or leukocyte immunoglobulin-like receptor (LILR) collections as well as various framing genes. This complex region is well described in hum...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1197687/full |
| _version_ | 1797829975666065408 |
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| author | April L. Jelinek Jan Futas Jan Futas Pamela A. Burger Petr Horin Petr Horin |
| author_facet | April L. Jelinek Jan Futas Jan Futas Pamela A. Burger Petr Horin Petr Horin |
| author_sort | April L. Jelinek |
| collection | DOAJ |
| description | BackgroundThe mammalian Leukocyte Receptor Complex (LRC) chromosomal region may contain gene families for the killer cell immunoglobulin-like receptor (KIR) and/or leukocyte immunoglobulin-like receptor (LILR) collections as well as various framing genes. This complex region is well described in humans, mice, and some domestic animals. Although single KIR genes are known in some Carnivora, their complements of LILR genes remain largely unknown due to obstacles in the assembly of regions of high homology in short-read based genomes.MethodsAs part of the analysis of felid immunogenomes, this study focuses on the search for LRC genes in reference genomes and the annotation of LILR genes in Felidae. Chromosome-level genomes based on single-molecule long-read sequencing were preferentially sought and compared to representatives of the Carnivora.ResultsSeven putatively functional LILR genes were found across the Felidae and in the Californian sea lion, four to five genes in Canidae, and four to nine genes in Mustelidae. They form two lineages, as seen in the Bovidae. The ratio of functional genes for activating LILRs to inhibitory LILRs is slightly in favor of inhibitory genes in the Felidae and the Canidae; the reverse is seen in the Californian sea lion. This ratio is even in all of the Mustelidae except the Eurasian otter, which has a predominance of activating LILRs. Various numbers of LILR pseudogenes were identified.ConclusionsThe structure of the LRC is rather conservative in felids and the other Carnivora studied. The LILR sub-region is conserved within the Felidae and has slight differences in the Canidae, but it has taken various evolutionary paths in the Mustelidae. Overall, the process of pseudogenization of LILR genes seems to be more frequent for activating receptors. Phylogenetic analysis found no direct orthologues across the Carnivora which corroborate the rapid evolution of LILRs seen in mammals. |
| first_indexed | 2024-04-09T13:29:48Z |
| format | Article |
| id | doaj.art-9a46cc3c6db241c180883a58ddcadb75 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-09T13:29:48Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-9a46cc3c6db241c180883a58ddcadb752023-05-10T05:12:46ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-05-011410.3389/fimmu.2023.11976871197687Comparative genomics of the Leukocyte Receptor Complex in carnivoresApril L. Jelinek0Jan Futas1Jan Futas2Pamela A. Burger3Petr Horin4Petr Horin5Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno (VETUNI), Brno, CzechiaDepartment of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno (VETUNI), Brno, CzechiaResearch Group Animal Immunogenomics, Central European Institute of Technology (CEITEC) VETUNI, Brno, CzechiaResearch Institute of Wildlife Ecology, University of Veterinary Medicine Vienna (VETMEDUNI), Vienna, AustriaDepartment of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno (VETUNI), Brno, CzechiaResearch Group Animal Immunogenomics, Central European Institute of Technology (CEITEC) VETUNI, Brno, CzechiaBackgroundThe mammalian Leukocyte Receptor Complex (LRC) chromosomal region may contain gene families for the killer cell immunoglobulin-like receptor (KIR) and/or leukocyte immunoglobulin-like receptor (LILR) collections as well as various framing genes. This complex region is well described in humans, mice, and some domestic animals. Although single KIR genes are known in some Carnivora, their complements of LILR genes remain largely unknown due to obstacles in the assembly of regions of high homology in short-read based genomes.MethodsAs part of the analysis of felid immunogenomes, this study focuses on the search for LRC genes in reference genomes and the annotation of LILR genes in Felidae. Chromosome-level genomes based on single-molecule long-read sequencing were preferentially sought and compared to representatives of the Carnivora.ResultsSeven putatively functional LILR genes were found across the Felidae and in the Californian sea lion, four to five genes in Canidae, and four to nine genes in Mustelidae. They form two lineages, as seen in the Bovidae. The ratio of functional genes for activating LILRs to inhibitory LILRs is slightly in favor of inhibitory genes in the Felidae and the Canidae; the reverse is seen in the Californian sea lion. This ratio is even in all of the Mustelidae except the Eurasian otter, which has a predominance of activating LILRs. Various numbers of LILR pseudogenes were identified.ConclusionsThe structure of the LRC is rather conservative in felids and the other Carnivora studied. The LILR sub-region is conserved within the Felidae and has slight differences in the Canidae, but it has taken various evolutionary paths in the Mustelidae. Overall, the process of pseudogenization of LILR genes seems to be more frequent for activating receptors. Phylogenetic analysis found no direct orthologues across the Carnivora which corroborate the rapid evolution of LILRs seen in mammals.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1197687/fullLeukocyte Receptor ComplexKIRLILRcarnivoralong-read sequencingfelids |
| spellingShingle | April L. Jelinek Jan Futas Jan Futas Pamela A. Burger Petr Horin Petr Horin Comparative genomics of the Leukocyte Receptor Complex in carnivores Frontiers in Immunology Leukocyte Receptor Complex KIR LILR carnivora long-read sequencing felids |
| title | Comparative genomics of the Leukocyte Receptor Complex in carnivores |
| title_full | Comparative genomics of the Leukocyte Receptor Complex in carnivores |
| title_fullStr | Comparative genomics of the Leukocyte Receptor Complex in carnivores |
| title_full_unstemmed | Comparative genomics of the Leukocyte Receptor Complex in carnivores |
| title_short | Comparative genomics of the Leukocyte Receptor Complex in carnivores |
| title_sort | comparative genomics of the leukocyte receptor complex in carnivores |
| topic | Leukocyte Receptor Complex KIR LILR carnivora long-read sequencing felids |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1197687/full |
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