TY - JOUR

T1 - Genome organization of major tandem repeats and their specificity for heterochromatin of macro- and microchromosomes in Japanese quail

AU - Цуканова, Ксения Николаевна

AU - Галкина, Светлана Анатольевна

AU - Кулак, Мария Михайловна

AU - Комиссаров, Алексей Сергеевич

AU - Сайфитдинова, Алсу Фаритовна

AU - Fillon, Valerie

N1 - Publisher Copyright: © 2022 The Author(s).

PY - 2022/7/1

Y1 - 2022/7/1

N2 - 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.

AB - 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.

KW - ADN satellite

KW - Coturnix japonica

KW - analyse de séquences brutes

KW - centromere

KW - centromère

KW - chromosomes en écouvillon

KW - lampbrush chromosomes

KW - satellite DNA

KW - sequencing raw reads analysis

UR - http://www.scopus.com/inward/record.url?scp=85137008533&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/fca69da7-f200-3732-883f-b5c832df85a6/

U2 - 10.1139/gen-2022-0012

DO - 10.1139/gen-2022-0012

M3 - Article

VL - 65

SP - 391

EP - 403

JO - Genome

JF - Genome

SN - 0831-2796

IS - 7

ER -