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Nat Commun. 2019 Jan 2;10(1):4. doi: 10.1038/s41467-018-07885-5.

Selective single molecule sequencing and assembly of a human Y chromosome of African origin.

Author information

1
Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain. lukas.kuderna@upf.edu.
2
Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain. esther.lizano@upf.edu.
3
Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Carrer del Doctor Aiguader 88, PRBB Building, Barcelona, 08003, Spain.
4
Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.
5
CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain.
6
Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain.
7
Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain.
8
Bioinformatics Research Center, Aarhus University, C.F. Moellers Alle 8, DK-8000 Aarhus C, Denmark.
9
Department of Bioscience, Aarhus University, Ny Munkegade 116, DK-8000 Aarhus C, Denmark.
10
Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain. tomas.marques@upf.edu.
11
CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain. tomas.marques@upf.edu.
12
Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain. tomas.marques@upf.edu.
13
Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Catalonia, 08010, Spain. tomas.marques@upf.edu.
14
Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona, 08193, Spain. tomas.marques@upf.edu.

Abstract

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes.

PMID:
30602775
PMCID:
PMC6315018
DOI:
10.1038/s41467-018-07885-5
[Indexed for MEDLINE]
Free PMC Article

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