ArticleGenome research2022
Gene prediction in the immunoglobulin loci.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 37 citations in OpenAlex.
- Characterization of immunoglobulin loci inNAR genomics and bioinformatics · 2026Article
- Immunoglobulin heavy chain locus duplication in bats.Science advances · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions.Bioinformatics (Oxford, England) · 2026Article
- Unraveling IGK locus in dog breeds: IMGTNAR genomics and bioinformatics · 2026Article
- Immunoglobulin germline reference sequences enable investigations and reveal insights into bat-specific immunity.iScience · 2025Article
- Gene discovery and expression analysis of the B cell receptor repertoire in the domestic ferret model.Vaccine · 2025Article
- PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences.Bioinformatics (Oxford, England) · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- From benchmarking alignment of genome assemblies to IMGT annotation: the paradigm of the bovine Bos taurus T cell receptor (TRG) locus.BMC genomics · 2025Article
- Comparative Analysis of Mammalian Adaptive Immune Loci Revealed Spectacular Divergence and Common Genetic Patterns.Molecular biology and evolution · 2025Article
- CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies.Genome biology · 2025Article
- ALIGaToR: A tool for the automated annotation of immunoglobulin and T cell receptor genomic loci.bioRxiv : the preprint server for biology · 2025Article
- Complete sequencing of ape genomes.Nature · 2025Article
- Different Species of Bats: Genomics, Transcriptome, and Immune Repertoire.Current issues in molecular biology · 2025Review
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
- ALIGaToR: a tool for the automated annotation of immunoglobulin and T cell receptor genomic loci.Oxford open immunology · 2025Article
- Complete sequencing of ape genomes.bioRxiv : the preprint server for biology · 2024Article
- Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- Evaluating methods for B-cell clonal family assignment.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The V(D)J recombination process rearranges the variable (V), diversity (D), and joining (J) genes in the immunoglobulin (IG) loci to generate antibody repertoires. Annotation of these loci across various species and predicting the V, D, and J genes (IG genes) are critical for studies of the adaptive immune system. However, because the standard gene finding algorithms are not suitable for predicting IG genes, they have been semimanually annotated in very few species. We developed the IGDetective algorithm for predicting IG genes and applied it to species with the assembled IG loci. IGDetective generated the first large collection of IG genes across many species and enabled their evolutionary analysis, including the analysis of the "bat IG diversity" hypothesis. This analysis revealed extremely conserved V genes in evolutionary distant species, indicating that these genes may be subjected to the same selective pressure, for example, pressure driven by common pathogens. IGDetective also revealed extremely diverged V genes and a new family of evolutionary conserved V genes in bats with unusual noncanonical cysteines. Moreover, unlike all other previously reported antibodies, these cysteines are located within complementarity-determining regions. Because cysteines form disulfide bonds, we hypothesize that these cysteine-rich V genes might generate antibodies with noncanonical conformations and could potentially form a unique part of the immune repertoire in bats. We also analyzed the diversity landscape of the recombination signal sequences and revealed their features that trigger the high/low usage of the IG genes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.