New high copy tandem repeat in the content of the chicken W chromosome
The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA)n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA)n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.
KeywordsSatellite DNA Raw reads analysis Kmer analysis Tandem repeats Gallus gallus Domesticus Lampbrush chromosomes
Council for International Organizations of Medical Sciences
Chicken repeat 1
Gallus_gallus-4.0 assembly of the chicken genome (GCA_000002315.2)
Gallus_gallus-5.0 assembly of the chicken genome (GCA_000002315.3)
Billions of base pairs
International Chicken Genome Sequencing Consortium
Long interspersed element
Long terminal repeat
Millions of base pairs
Nucleolus organizer region
Short interspersed element
Sodium salt citrate
Tandem repeat finder
We are grateful to the anonymous Reviewers for their very useful comments and suggestions. The authors acknowledge Dr. Irina Solovei for providing plasmids pUGD0600 and pUGD1202. We would like to thank Dr. Denis Bogomaz for his assistance in oligonucleotide synthesis and Dr. Inna Kuznetsova for her fruitful discussion. This work was supported by the grant from Russian Foundation for Basic Research (16-04-01823). Aleksey Komissarov and Stephen O’Brien are financially supported by Russian Science Foundation (17-14-01138). The postdoctoral fellowship from St. Petersburg State University was provided for Elena I. Koshel (1.50.1043.2014). The equipment and software of Chromas Research Resource Center and Theodosius Dobzhansky Centre for Genome Bioinformatics of Saint Petersburg State University were used.
This study was funded by the grant from Russian Foundation for Basic Research (16–04-01823).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest regarding the publication of this paper.
Animal rights statement
All procedures performed in studies involving animals were in accordance with International Guiding Principles for Biomedical Research Involving Animals established by Council for International Organizations of Medical Sciences (CIOMS) and approved by Saint-Petersburg State University Ethics Committee (statement # 131–03-2).
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