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Gene prediction in the immunoglobulin loci
Vikram Sirupurapu1, Yana Safonova1,2, Pavel A Pevzner1
1Computer Science and Engineering Department, University of California San Diego, San Diego, California 92093, USA.
Genome Research
|May 11, 2022
Summary
IGDetective algorithm predicts immunoglobulin (IG) genes, enabling the first large-scale evolutionary analysis of antibody diversity across species. It revealed conserved genes under pathogen pressure and unique cysteine-rich genes in bats.
Area of Science:
- Immunology
- Bioinformatics
- Evolutionary Biology
Background:
- V(D)J recombination is crucial for generating antibody diversity.
- Standard gene-finding algorithms are inadequate for immunoglobulin (IG) gene prediction.
- Manual annotation of IG loci is limited to a few species.
Purpose of the Study:
- Develop a novel algorithm, IGDetective, for accurate IG gene prediction.
- Enable large-scale evolutionary analysis of IG genes across diverse species.
- Investigate the "bat IG diversity" hypothesis and identify unique features of bat antibodies.
Main Methods:
- Developed the IGDetective algorithm for IG gene prediction.
- Applied IGDetective to assembled IG loci from various species.
- Performed evolutionary analysis of predicted IG genes and recombination signal sequences.
Main Results:
- Generated the first extensive collection of IG genes across multiple species.
- Identified highly conserved V genes in evolutionarily distant species, suggesting shared selective pressures (e.g., from pathogens).
- Discovered novel, conserved, cysteine-rich V genes in bats with unusual features within complementarity-determining regions, potentially leading to unique antibody conformations.
Conclusions:
- IGDetective significantly advances the study of adaptive immunity by enabling comprehensive IG gene annotation and evolutionary analysis.
- Conserved IG genes highlight the impact of common pathogens on immune system evolution.
- Unique cysteine-rich antibodies in bats may represent a specialized component of their immune repertoire, warranting further investigation into their structure and function.
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