High-resolution characterization of the structural features and genetic variation of six feline leukocyte antigen class I loci via single molecule, real-time (SMRT) sequencing

Holmes, Jennifer C.; Scholl, Elizabeth H.; Dickey, Allison N.; Hess, Paul R.

doi:10.1007/s00251-021-01221-w

Cited by 4 publications

(3 citation statements)

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“…It seems that in the cat and the dog, the subregions corresponding to HLA-A and HLA- E in humans have been lost ( Yuhki et al, 2007 ). Currently, FLA-E , FLA-H and FLA-K are classified as classical, while FLA-A , FLA-J , FLA-L , and FLA-O are considered non-classical class I genes ( Holmes et al, 2021 ). Due to gene conversion and duplication events occurring during the process of diversification of class I genes, it is not possible to directly extrapolate from orthologous HLA or H-2 class I genes to define the classical/non-classical status of the FLA class I genes.…”

Section: Comparative Major Histocompatibility Complex Genomics Of Felidsmentioning

confidence: 99%

“…Due to the complexity of the rapid birth-and-death process resulting in multiple new MHC class I genes, it is not possible to directly extrapolate from orthologous HLA or H-2 class I genes to define the classical/non-classical status of the FLA class I genes and thus to identify putative NKR ligands. Considering the strong structural conservation of class I molecules reflecting common functional demands, genetic features related to their function may be used to distinguish between classical and non-classical genes and molecules ( Holmes et al, 2021 ). For this purpose, knowledge of their receptors can provide important information, and therefore not only the MHC but also NKR loci should be properly annotated in the genomes of felids and characterized.…”

Section: A Reverse View Perspective On the Biology Of Major Histocomp...mentioning

confidence: 99%

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Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids

et al. 2022

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This review summarizes the current knowledge on the major histocompatibility complex (MHC) of the family Felidae. This family comprises an important domestic species, the cat, as well as a variety of free-living felids, including several endangered species. As such, the Felidae have the potential to be an informative model for studying different aspects of the biological functions of MHC genes, such as their role in disease mechanisms and adaptation to different environments, as well as the importance of genetic diversity for conservation issues in free-ranging or captive populations. Despite this potential, the current knowledge on the MHC in the family as a whole is fragmentary and based mostly on studies of the domestic cat and selected species of big cats. The overall structure of the domestic cat MHC is similar to other mammalian MHCs following the general scheme “centromere-MHC class I-MHC class III-MHC class II” with some differences in the gene contents. An unambiguously defined orthologue of the non-classical class I HLA-E gene has not been identified so far and the class II DQ and DP genes are missing or pseudogenized, respectively. A comparison with available genomes of other felids showed a generally high level of structural and sequence conservation of the MHC region. Very little and fragmentary information on in vitro and/or in vivo biological functions of felid MHC genes is available. So far, no association studies have indicated effects of MHC genetic diversity on a particular disease. No information is available on the role of MHC class I molecules in interactions with Natural Killer (NK) cell receptors or on the putative evolutionary interactions (co-evolution) of the underlying genes. A comparison of complex genomic regions encoding NK cell receptors (the Leukocyte Receptor Complex, LRC and the Natural Killer Cell Complex, NKC) in the available felid genomes showed a higher variability in the NKC compared to the LRC and the MHC regions. Studies of the genetic diversity of domestic cat populations and/or specific breeds have focused mainly on DRB genes. Not surprisingly, higher levels of MHC diversity were observed in stray cats compared to pure breeds, as evaluated by DRB sequencing as well as by MHC-linked microsatellite typing. Immunogenetic analysis in wild felids has only been performed on MHC class I and II loci in tigers, Namibian leopards and cheetahs. This information is important as part of current conservation tasks to assess the adaptive potential of endangered wild species at the human-wildlife interface, which will be essential for preserving biodiversity in a functional ecosystem.

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Section: Comparative Major Histocompatibility Complex Genomics Of Felidsmentioning

confidence: 99%

Section: A Reverse View Perspective On the Biology Of Major Histocomp...mentioning

confidence: 99%

Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids

et al. 2022

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“…Fortunately, full-length transcriptome sequencing has been employed as an effective approach to obtain high-quality transcript sequences in the absence of reference genomes. Single-molecule real-time (SMRT) sequencing developed by Pacific Biosciences (PacBio) can obtain full-length sequences without post-sequencing assembly (Holmes et al, 2021), which has been used for wholetranscriptome profiling in many crustaceans (Cao et al, 2020;Ren et al, 2020;Zheng et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analysis Provide Insights Into the Ovarian Maturation of Exopalaemon carinicauda

Wang

Li²,

Ge³

et al. 2022

Front. Mar. Sci.

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The ridgetail white shrimp Exopalaemon carinicauda has the potential to be used as a useful experimental organism in the field of crustacean research due to its transparent body, large egg, and short reproductive cycle. However, little is known about the regulatory mechanisms of ovarian maturation in E. carinicauda. In this study, we applied PacBio single-molecule long-read sequencing technology to unveil the whole transcriptome landscape of Exopalaemon carinicauda to better understand the molecular mechanisms of ovarian development. A total of 49.05 G polymerase read bases were generated, finally, 15, 151 unigenes were successfully identified with a mean length of 4, 257 bp and an N50 of 4, 884 bp from ovary tissues (five different ovarian developmental stages). A total of 14, 007 unigenes were successfully annotated in at least one public database. In addition, 8, 861 coding sequences, 4, 594 lncRNAs and 895 transcription factors were identified. Furthermore, we performed RNA-Seq analysis combined with Iso-Seq results to investigate ovarian maturation regulation mechanism and validated the results by quantitative real-time PCR. We annotated five vitellogenin isoforms in the full-length transcriptome, meanwhile these five genes and vitellogenin receptor suggested an important role during previtellogenesis of E. carinicauda. Genes were involved in PI3K-Akt signaling pathway, retinol metabolism, cell cycle and hedgehog signaling pathway, which showed obvious associations with ovarian maturation of E. carinicauda. We identified 40 DEGs, such as forkhead box protein L2, which may be related to ovarian development in the comparisons. The expression profiles of genes such as ecdysone receptor, ecdysone-induced protein 74EF, ecdysone inducible gene E75 and post-molt protein suggest that they were significantly associated with reproductive molting in the ovarian mature stage. In conclusion, the present study identified important genes and pathways involved in ovarian maturation, which might be useful for studying the reproductive regulation and mechanisms of ovarian maturation in E. carinicauda.

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Feliformes: The cats and their relatives

Tizard

2023

Comparative Mammalian Immunology

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High-resolution characterization of the structural features and genetic variation of six feline leukocyte antigen class I loci via single molecule, real-time (SMRT) sequencing

Cited by 4 publications

References 54 publications

Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids

Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids

Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analysis Provide Insights Into the Ovarian Maturation of Exopalaemon carinicauda

Feliformes: The cats and their relatives

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