# An Exceptionally Complex Chromosome Rearrangement in the Great Tit (Parus major): Genetic Composition, Meiotic Behavior and Population Frequency

## TL;DR

A complex chromosome rearrangement in great tits includes a large inversion and gene amplification, offering insights into genomic evolution and adaptation.

## Contribution

The discovery of a novel 55 Mb inversion and 30 Mb amplification on great tit chromosome 1A, including a 50,000-copy tandem repeat of FAM118A.

## Key findings

- A complex rearrangement on chromosome 1A is present in 19% of Siberian great tits and 5% of European birds.
- The rearrangement includes a 55 Mb inversion and a 30 Mb amplification with a 630 bp tandem repeat expanded to ~50,000 copies.
- The amplified region is homologous to FAM118A, a gene linked to immune function, and is missing from the current reference genome.

## Abstract

What are the main findings?
A complex rearrangement on chromosome 1A, combining a ~55 Mb inversion and >30 Mb of copy-number expansion, is present in ~19% of the great tits in the Siberian population. A similar rearrangement has been previously detected in 5% of birds in the European population.The amplified region includes a sequence homologous to the FAM118A locus conserved in vertebrates with a nested 630 bp tandem repeat, expanded to ~50,000 copies in the rearranged chromosome.

A complex rearrangement on chromosome 1A, combining a ~55 Mb inversion and >30 Mb of copy-number expansion, is present in ~19% of the great tits in the Siberian population. A similar rearrangement has been previously detected in 5% of birds in the European population.

The amplified region includes a sequence homologous to the FAM118A locus conserved in vertebrates with a nested 630 bp tandem repeat, expanded to ~50,000 copies in the rearranged chromosome.

What are the implications of the main findings?
The rearranged chromosome provides a natural system to investigate the genomic consequences and evolutionary maintenance of large inversion–amplification complexes.The FAM118A expansion provides a framework for assessing potential functional and adaptive effects of extreme gene amplification in a wild population.

The rearranged chromosome provides a natural system to investigate the genomic consequences and evolutionary maintenance of large inversion–amplification complexes.

The FAM118A expansion provides a framework for assessing potential functional and adaptive effects of extreme gene amplification in a wild population.

Chromosomal inversions and copy-number variants (CNVs) drive genomic and phenotypic diversification in birds by reshaping recombination, gene expression, and genome architecture. Here, we report a complex structural polymorphism on great tit (Parus major) chromosome 1A that occurs in the Siberian population with a 19% heterozygote frequency. Using cytogenetic and genomic approaches, we show that this rearrangement combines a ~55 Mb paracentric inversion in the long arm with a dramatic (>30 Mb) expansion of the short arm driven by extensive amplification of multiple genomic loci. These include a region homologous to the poorly characterized FAM118A gene, whose paralog FAM118B has been recently shown to play a pivotal role in innate immune activation. This region is missing from the current reference genome assembly while present in ~20 copies on wild-type 1A chromosome and nearly twentyfold amplified in the rearranged variant. It contains a nested 630 bp tandem repeat, encompassing the entire exon 3, which has burst to a total of ~50,000 copies in the rearranged chromosome. While functional analyses are required to uncover the biological effects of the genomic features linked to this rearrangement, our results offer a unique framework for studying how complex structural polymorphisms drive genome innovation and adaptive diversity.