Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes.
2018
Аутори:
Makunin, Alexey I.Rajičić, Marija
Karamysheva, Tatyana V.
Romanenko, Svetlana A.
Druzhkova, Anna S.
Blagojević, Jelena
Vujošević, Mladen
Rubtsov, Nikolay B.
Graphodatsky, Alexander S.
Trifonov, Vladimir A.
Тип документа:
Чланак у часопису (Објављена верзија)
,
© Springer-Verlag GmbH Germany, part of Springer Nature 2018
Метаподаци
Приказ свих података о документуАпстракт:
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.
Кључне речи:
Apodemus flavicollis; Apodemus peninsulae; Galaxy; Genome instability; PipelineИзвор:
Chromosoma, 2018, 127, 3, 301-311Финансирање / пројекти:
- Генетичка и фенетичка разноврсност у природним популацијама у различитим срединама - допринос полиморфизма Б хромозома (RS-MESTD-Basic Research (BR or ON)-173003)
DOI: 10.1007/s00412-018-0662-0
ISSN: 0009-5915
PubMed: 29380046
WoS: 000441098400003
Scopus: 2-s2.0-85041121433
URI
http://link.springer.com/10.1007/s00412-018-0662-0http://www.ncbi.nlm.nih.gov/pubmed/29380046
https://radar.ibiss.bg.ac.rs/handle/123456789/2969