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Chromosoma

, Volume 127, Issue 3, pp 301–311 | Cite as

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

  • Alexey I. Makunin
  • Marija Rajičić
  • Tatyana V. Karamysheva
  • Svetlana A. Romanenko
  • Anna S. Druzhkova
  • Jelena Blagojević
  • Mladen Vujošević
  • Nikolay B. Rubtsov
  • Alexander S. Graphodatsky
  • Vladimir A. Trifonov
Original Article

Abstract

Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes. Genetic content of both B-chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single chromosomes with subsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B chromosomes in mice Apodemus flavicollis and Apodemus peninsulae. The pipeline for sequencing data analysis was made available in Galaxy interface as an addition to previously published command-line version. Human sSMC was attributed to the proximal part of chromosome 15 long arm, and breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B chromosomes was species-specific, and minor alterations were observed in both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1. Understanding of the non-essential genome elements content provides important insights into genome evolution in general.

Keywords

Genome instability Apodemus peninsulae Apodemus flavicollis Galaxy Pipeline 

Notes

Acknowledgments

We would like to thank Dr. Aleksey Bogdanov (Kol’tsov Institute of Developmental Biology RAS), Dr. Irina Kartavtseva (Institute of Biology and Soil Science FEB RAS), and Dr. Yuri Borissov (Severtsov Institute of Ecology and Evolution RAS) for providing animal samples and Fedor Goncharov (Institute of Molecular and Cellular Biology SB RAS) for IMCB Galaxy server maintenance. DNA sequencing was performed by the “Molecular and cellular biology” facility at IMCB SB RAS (Illumina) and by sequencing facility at ICG SB RAS (Ion Torrent).

Funding information

The study was supported by Russian Science Foundation grant 16-14-10009; by Ministry of Education, Science and Technological Development, Republic of Serbia, grant 173003; and by the project #0324-2016-0003 of the Institute Cytology and Genetics SB RAS.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human studies

All procedures performed in studies involving human participant were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from the individual participant included in the study.

Animal studies

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Supplementary material

412_2018_662_MOESM1_ESM.pdf (629 kb)
ESM 1 (PDF 629 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Alexey I. Makunin
    • 1
  • Marija Rajičić
    • 2
  • Tatyana V. Karamysheva
    • 3
  • Svetlana A. Romanenko
    • 1
    • 4
  • Anna S. Druzhkova
    • 1
    • 4
  • Jelena Blagojević
    • 2
  • Mladen Vujošević
    • 2
  • Nikolay B. Rubtsov
    • 3
  • Alexander S. Graphodatsky
    • 1
    • 4
  • Vladimir A. Trifonov
    • 1
    • 4
  1. 1.Institute of Molecular and Cellular Biology Siberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Institute for Biological Research “Siniša Stanković”University of BelgradeBelgradeSerbia
  3. 3.Institute of Cytology and Genetics Siberian Branch of the Russian Academy of SciencesNovosibirskRussia
  4. 4.Novosibirsk State UniversityNovosibirskRussia

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