# GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions

## TL;DR

This paper introduces a new algorithm called GenomeDecoder to study complex genomic regions and reveals rapid evolution in immunoglobulin genes across primates.

## Contribution

GenomeDecoder is a novel algorithm for inferring segmental duplications in highly repetitive genomic regions.

## Key findings

- GenomeDecoder identified rapid birth/death of immunoglobulin genes in human populations.
- Immunoglobulin loci show large architectural changes across primate genomes.
- Primate immunoglobulin loci are under diversifying selection.

## Abstract

The emergence of the ‘telomere-to-telomere’ genomics brought the challenge of identifying segmental duplications (SDs) in complete genomes. It further opened a possibility for identifying the differences in SDs across individual human genomes and studying the SD evolution. These newly emerged challenges require algorithms for reconstructing SDs in the most complex genomic regions that evaded all previous attempts to analyze their architecture, such as rapidly evolving immunoglobulin loci.

We describe the GenomeDecoder algorithm for inferring SDs and apply it to analyzing genomic architectures of various loci in primate genomes. Our analysis revealed that multiple duplications/deletions led to a rapid birth/death of immunoglobulin genes within the human population and large changes in genomic architecture of immunoglobulin loci across primate genomes. Comparison of immunoglobulin loci across primate genomes suggests that they are subjected to diversifying selection.

GenomeDecoder is available at https://github.com/ZhangZhenmiao/GenomeDecoder. The software version and test data used in this paper are uploaded to https://doi.org/10.5281/zenodo.14753844.