TY - JOUR

T1 - An Exceptionally Complex Chromosome Rearrangement in the Great Tit (Parus major): Genetic Composition, Meiotic Behavior and Population Frequency

AU - Torgasheva, Anna

AU - Malinovskaya, Lyubov

AU - Nuriddinov, Miroslav

AU - Zadesenets, Kira S.

AU - Gridina, Maria

AU - Nurislamov, Artem

AU - Korableva, Svetlana

AU - Pristyazhnyuk, Inna

AU - Proskuryakova, Anastasiya

AU - Tishakova, Katerina V.

AU - Rubtsov, Nikolay B.

AU - Fishman, Veniamin S.

AU - Borodin, Pavel

N1 - This research was funded by the Russian Science Foundation, grant number 23-14-00182. A.T. was supported by the Bonn Institute for Organismic Biology–Animal Diversity (University of Bonn).

PY - 2025/12/27

Y1 - 2025/12/27

N2 - 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.

AB - 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.

KW - FAM118A

KW - Hi-C

KW - chromosomal inversions

KW - copy number variation (CNV)

KW - genome evolution

KW - great tit

KW - recombination suppression

KW - structural variation

UR - https://www.scopus.com/pages/publications/105026994895

UR - https://www.mendeley.com/catalogue/40f05127-baca-320a-b51e-72649f880c30/

U2 - 10.3390/cells15010052

DO - 10.3390/cells15010052

M3 - Article

C2 - 41511336

VL - 15

JO - Cells

JF - Cells

SN - 2073-4409

IS - 1

M1 - 52

ER -