The natural cytotoxicity receptor genes in the family Felidae

Bubeníkova, Jana; Futas, Ján; Oppelt, Jan; Plášil, Martin; Vodička, Roman; Burger, Pamela A.; Hořín, Petr

doi:10.1111/tan.14803

Cited by 3 publications

(2 citation statements)

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“… * NCR1 appears to be pseudogenized in the reference assemblies of these species but has been shown to be functional ( 37 ). **In Lynx canadensis , GP6 was found in the WGS but not in the reference assembly.…”

Section: Resultsmentioning

confidence: 99%

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Comparative genomics of the Leukocyte Receptor Complex in carnivores

et al. 2023

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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.

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Section: Resultsmentioning

confidence: 99%

“…In all felids except the Canada lynx, an additional putatively functional 2-Ig inhibitory gene was found between GP6 and *NCR1 appears to be pseudogenized in the reference assemblies of these species but has been shown to be functional (37). **In Lynx canadensis, GP6 was found in the WGS but not in the reference assembly.…”

Section: Felidaementioning

confidence: 98%

Comparative genomics of the Leukocyte Receptor Complex in carnivores

et al. 2023

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Feline innate lymphoid cells

Tizard

2025

The Immunology of the Cat

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Identifying novel genetic and phenotypic associations to genomic features by leveraging off-target reads in exome sequencing data

Ercelen,

Caggiano,

Border

et al. 2024

Preprint

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Upwards of 40% of reads in sequencing datasets may be unmapped and discarded by standard protocols. Recent work has shown the utility of re-analyzing these unmapped reads to construct meaningful features, such as immune diversity repertoires or copy number variation in mtDNA and rDNA. While previous analyses of these features have produced significant correlations with diverse traits, they have generally been limited to analyses of RNA-sequencing data in phenotype-specific cohorts. Here, we explore whether associations can be identified using population-scale, whole-exome sequencing data in the UK BioBank. Using recently developed tools, we constructed multiple features including T-cell receptor diversity metrics, microbial load, and mtDNA and rDNA copy numbers for nearly 50,000 individuals in the UK BioBank. We first verify the validity of our method by showing that GWAS on these constructed traits results in replication of associations from studies in which the phenotypes were explicitly measured. Next, across several GWAS, we identified 21 novel independent significant loci in 11 genes, most of them in genes implicated in the innate immune response. Finally, we further analyzed the read-constructed features by establishing correlations to other population-level biobank traits such as immune disorders, metabolic disorders, neuropsychiatric disorders, and blood cell counts. Our results suggest that existing tools for feature construction from unmapped reads can offer novel information at the population level, and that these features can be used to establish novel genetic associations.

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The natural cytotoxicity receptor genes in the family Felidae

Cited by 3 publications

References 40 publications

Comparative genomics of the Leukocyte Receptor Complex in carnivores

Comparative genomics of the Leukocyte Receptor Complex in carnivores

Feline innate lymphoid cells

Identifying novel genetic and phenotypic associations to genomic features by leveraging off-target reads in exome sequencing data

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