Kulak Maria, Komissarov Aleksey, Fillon Valerie, Tsukanova Kseniya, Saifitdinova Alsu, Galkina Svetlana
Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb. 7/9, Saint Petersburg 199034, Russia.
Applied Genomics Laboratory, SCAMT Institute, ITMO University, Lomonosova str., 9, Saint Petersburg 191002, Russia.
Genome. 2022 Jul 1;65(7):391-403. doi: 10.1139/gen-2022-0012.
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 SAT primarily contributes to the centromeric regions of the macrochromosomes CJA1-8. 31B together with previously characterized II 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 84A, 408A, and SAT 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.
串联重复DNA形成染色体的异染色质区域，包括重要的着丝粒染色质。尽管新的基因组技术取得了进展，但串联重复序列仍然难以解读，需要在感兴趣的物种中进行靶向分析。日本鹌鹑是高产家禽物种之一，也是一种模式生物。其基因组因异染色质的显著积累而有所不同，与鸡的基因组大小相比增加了1/7。突出的异染色质块占据了近端着丝粒大染色体和微染色体的短臂。我们将从头重复序列查找方法应用于日本鹌鹑基因组未组装的原始读数。我们鉴定出20个最常见的串联重复序列，丰度>1 Mb，约占基因组的4.8%。我们发现串联重复序列SAT主要分布在大染色体CJA1-8的着丝粒区域。31B与先前鉴定的II一起构成了微染色体和W染色体的着丝粒区域。荧光原位杂交显示，其他重复序列以不同比例分布在微染色体短臂的异染色质中。84A、408A和SAT重复序列与逆转录转座子基序相似。这表明逆转录元件可能在日本鹌鹑基因组中重复序列的分布中起了关键作用。
