Research output: Contribution to journal › Article › peer-review
Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes. / Makunin, Alexey I.; Rajičić, Marija; Karamysheva, Tatyana V. et al.
In: Chromosoma, Vol. 127, No. 3, 01.09.2018, p. 301-311.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes
AU - Makunin, Alexey I.
AU - Rajičić, Marija
AU - Karamysheva, Tatyana V.
AU - Romanenko, Svetlana A.
AU - Druzhkova, Anna S.
AU - Blagojević, Jelena
AU - Vujošević, Mladen
AU - Rubtsov, Nikolay B.
AU - Graphodatsky, Alexander S.
AU - Trifonov, Vladimir A.
N1 - Publisher Copyright: © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.
PY - 2018/9/1
Y1 - 2018/9/1
N2 - 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.
AB - 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.
KW - Apodemus flavicollis
KW - Apodemus peninsulae
KW - Galaxy
KW - Genome instability
KW - Pipeline
KW - PENINSULAE
KW - REARRANGEMENTS
KW - GENOME
KW - BREAKPOINTS
KW - MICROCHROMOSOME
KW - EVOLUTION
KW - DNA
KW - FISH
KW - GENERATION
KW - MICRODISSECTION
UR - http://www.scopus.com/inward/record.url?scp=85041121433&partnerID=8YFLogxK
U2 - 10.1007/s00412-018-0662-0
DO - 10.1007/s00412-018-0662-0
M3 - Article
C2 - 29380046
AN - SCOPUS:85041121433
VL - 127
SP - 301
EP - 311
JO - Chromosoma
JF - Chromosoma
SN - 0009-5915
IS - 3
ER -
ID: 9327707