Genome organization of major tandem repeats and their specificity for heterochromatin of macro- and microchromosomes in Japanese quail

Author:

Kulak Maria1,Komissarov Aleksey2,Fillon Valerie3,Tsukanova Kseniya1,Saifitdinova Alsu4,Galkina Svetlana1ORCID

Affiliation:

1. Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb. 7/9, Saint Petersburg 199034, Russia

2. Applied Genomics Laboratory, SCAMT Institute, ITMO University, Lomonosova str., 9, Saint Petersburg 191002, Russia

3. GenPhySE, Université de Toulouse, INRA Toulouse-Occitanie, ENVT, 24 chemin de Borde-Rouge, 31326 Castanet Tolosan, France

4. Department of Human and Animal Anatomy and Physiology, Herzen State Pedagogical University of Russia, Moyka emb. 48, Saint Petersburg 191186, Russia

Abstract

Tandemly repeated DNAs form heterochromatic regions of chromosomes, including the vital centromeric chromatin. Despite the progress in new genomic technologies, tandem repeats remain poorly deciphered and need targeted analysis in the species of interest. The Japanese quail is one of the highest-producing poultry species as well as a model organism. Its genome differs by a noticeable accumulation of heterochromatin, which led to an increase by 1/7 compared to the chicken genome size. Prominent heterochromatin blocks occupy the short arms of acrocentric macrochromosomes and of microchromosomes. We have applied de novo repeat finder approach to unassembled raw reads of the Japanese quail genome. We identified the 20 most common tandem repeats with the abundance >1 Mb, which represent about 4.8% of the genome. We found that tandem repeat CjapSAT primarily contributes to the centromeric regions of the macrochromosomes CJA1–8. Cjap31B together with previously characterized BglII makes up centromere regions of microchromosomes and W chromosome. Other repeats populate heterochromatin of microchromosomal short arms in unequal proportions, as revealed by fluorescence in situ hybridization. The Cjap84A, Cjap408A, and CjapSAT repeat sequences show similarities to retrotransposon motifs. This suggests that retroelements may have played a crucial role in the distribution of repeats throughout the Japanese quail genome.

Funder

Russian Science Foundation

Publisher

Canadian Science Publishing

Subject

Genetics,Molecular Biology,General Medicine,Biotechnology

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