Four immunoglobulin isotypes and IgD splice variants in urodele amphibians

Yoshinaga, Keisuke; Oshio, H; Prasetio, Billy; Hayashida, Haruka; Maeda, Eriko; Matsumoto, Mizuki

doi:10.1016/j.dci.2020.103963

Cited by 3 publications

(2 citation statements)

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“…Apart from such inconsistencies, the overall organization of the Ig loci in A. mexicanum is similar to the anuran X. tropicalis, and we confirmed studies describing the main antibody classes, IgM and IgY (34), IgX (35) and IgD (36). Interestingly we demonstrate that IGHF is a pseudogene.…”

Section: Discussionsupporting

confidence: 86%

Characterization of immunoglobulin loci in the gigantic genome of Ambystoma mexicanum

et al. 2023

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BackgroundThe axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model vertebrates.MethodsThe most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other vertebrates. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human, Xenopus tropicalis, Danio rerio (zebrafish), and eight tetrapod reference genomes were used for comparison.ResultsCanonical A. mexicanum heavy chain (IGH), lambda (IGL), sigma (IGS), and the putative surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes and there is no clan I IGHV genes. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality.ConclusionThe A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of Ig gene loss which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response.

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Section: Discussionsupporting

confidence: 86%

Characterization of immunoglobulin loci in the gigantic genome of Ambystoma mexicanum

et al. 2023

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show abstract

“…Apart from such inconsistencies, the overall organization of the Ig loci in A. mexicanum is similar to the anuran X. tropicalis , and we confirmed studies describing the main antibody classes, IgM and IgY (Fellah, Jacques, and Charlemagne 1994), IgX (Schaerlinger and Frippiat 2008) and IgD (Yoshinaga et al 2021). Interestingly we demonstrate that IGHF is a pseudogene.…”

Section: Discussionsupporting

confidence: 86%

Subfunctionalization and constrained size of the immunoglobulinlociinAmbystoma mexicanum

Martínez-Barnetche

Godoy-Lozano

Remy-Hernández

et al. 2022

Preprint

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Background: The axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model tetrapods. Methods: The most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other tetrapods. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human reference genomes, Xenopus tropicalis, and Danio rerio (zebrafish) were used for comparison. Results: Canonical A. mexicanum Heavy chain (IGH), lambda (IGL), sigma (IGS) and Surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes, there are no clan I IGHV genes and CDRH3 diversity is restricted. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and in the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality. Conclusion: The A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of pseudogenization which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response.

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