Chromosoma

pp 1–11 | Cite as

New high copy tandem repeat in the content of the chicken W chromosome

  • Aleksey S. Komissarov
  • Svetlana A. Galkina
  • Elena I. Koshel
  • Maria M. Kulak
  • Aleksander G. Dyomin
  • Stephen J. O’Brien
  • Elena R. Gaginskaya
  • Alsu F. Saifitdinova
Original Article

Abstract

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.

Keywords

Satellite DNA Raw reads analysis Kmer analysis Tandem repeats Gallus gallus Domesticus Lampbrush chromosomes 

Abbreviations

CIOMS

Council for International Organizations of Medical Sciences

CR1

Chicken repeat 1

DAPI

4′,6-diamidino-2-phenylindole

Galgal4

Gallus_gallus-4.0 assembly of the chicken genome (GCA_000002315.2)

Galgal5

Gallus_gallus-5.0 assembly of the chicken genome (GCA_000002315.3)

Gb

Billions of base pairs

ICGSC

International Chicken Genome Sequencing Consortium

LINE

Long interspersed element

LTR

Long terminal repeat

Mb

Millions of base pairs

NOR

Nucleolus organizer region

SINE

Short interspersed element

SSC

Sodium salt citrate

TRF

Tandem repeat finder

Notes

Acknowledgements

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.

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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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Aleksey S. Komissarov
    • 1
  • Svetlana A. Galkina
    • 2
    • 3
  • Elena I. Koshel
    • 4
  • Maria M. Kulak
    • 4
  • Aleksander G. Dyomin
    • 3
    • 5
  • Stephen J. O’Brien
    • 1
    • 6
  • Elena R. Gaginskaya
    • 4
  • Alsu F. Saifitdinova
    • 5
    • 7
  1. 1.Theodosius Dobzhansky Center for Genome BioinformaticsSaint Petersburg State UniversitySaint PetersburgRussia
  2. 2.Department of Genetics and BiotechnologySaint Petersburg State UniversitySaint PetersburgRussia
  3. 3.Saint Petersburg Association of Scientists and ScholarsSaint PetersburgRussia
  4. 4.Department of Cytology and HistologySaint Petersburg State UniversitySaint PetersburgRussia
  5. 5.Chromas Research Resource CenterSaint Petersburg State UniversitySaint PetersburgRussia
  6. 6.Oceanographic CenterNova Southeastern UniversityFloridaUSA
  7. 7.International Centre of Reproductive MedicineSaint PetersburgRussia

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