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

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  • Lukas F. K. Kuderna, Univ Pompeu Fabra, Pompeu Fabra University, CSIC-UPF - Institut de Biologia Evolutiva (IBE), Consejo Superior de Investigaciones Cientificas (CSIC), Inst Biol Evolut, CSIC, PRBB
  • ,
  • Esther Lizano, Univ Pompeu Fabra, Pompeu Fabra University, CSIC-UPF - Institut de Biologia Evolutiva (IBE), Consejo Superior de Investigaciones Cientificas (CSIC), Inst Biol Evolut, CSIC, PRBB
  • ,
  • Eva Julia, Barcelona Inst Sci & Technol, Pompeu Fabra University, Centre de Regulacio Genomica (CRG), Barcelona Institute of Science & Technology, Ctr Genom Regulat CRG
  • ,
  • Jessica Gomez-Garrido, Barcelona Inst Sci & Technol, Barcelona Institute of Science & Technology, Centre de Regulacio Genomica (CRG), Pompeu Fabra University, CNAG CRG, Ctr Genom Regulat CRG
  • ,
  • Aitor Serres-Armero, Univ Pompeu Fabra, Pompeu Fabra University, CSIC-UPF - Institut de Biologia Evolutiva (IBE), Consejo Superior de Investigaciones Cientificas (CSIC), Inst Biol Evolut, CSIC, PRBB
  • ,
  • Martin Kuhlwilm, Univ Pompeu Fabra, Pompeu Fabra University, CSIC-UPF - Institut de Biologia Evolutiva (IBE), Consejo Superior de Investigaciones Cientificas (CSIC), Inst Biol Evolut, CSIC, PRBB
  • ,
  • Regina Antoni Alandes, Barcelona Inst Sci & Technol, Barcelona Institute of Science & Technology, Centre de Regulacio Genomica (CRG), Pompeu Fabra University, CNAG CRG, Ctr Genom Regulat CRG
  • ,
  • Marina Alvarez-Estape, Univ Pompeu Fabra, Pompeu Fabra University, CSIC-UPF - Institut de Biologia Evolutiva (IBE), Consejo Superior de Investigaciones Cientificas (CSIC), Inst Biol Evolut, CSIC, PRBB
  • ,
  • David Juan, Univ Pompeu Fabra, Pompeu Fabra University, CSIC-UPF - Institut de Biologia Evolutiva (IBE), Consejo Superior de Investigaciones Cientificas (CSIC), Inst Biol Evolut, CSIC, PRBB
  • ,
  • Heath Simon, UPF, Pompeu Fabra University
  • ,
  • Tyler Alioto, UPF, Pompeu Fabra University
  • ,
  • Marta Gut, UPF, Pompeu Fabra University
  • ,
  • Ivo Gut, UPF, Pompeu Fabra University
  • ,
  • Mikkel Heide Schierup
  • Oscar Fornas, UPF, Pompeu Fabra University
  • ,
  • Tomas Marques-Bonet, Univ Autonoma Barcelona, Autonomous University of Barcelona, Institut Catala de Paleontologia Miquel Crusafont (ICP), Inst Catala Paleontol Miquel Crusafont

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.

Original languageEnglish
Article number4
JournalNature Communications
Volume10
Issue1
Number of pages8
ISSN2041-1723
DOIs
Publication statusPublished - 2019

    Research areas

  • LARGE GENOMES, ACCURATE, ALIGNMENT, EVOLUTION, VERSATILE, Humans, Molecular Sequence Annotation, African Continental Ancestry Group/genetics, Sequence Analysis, DNA, Chromosomes, Human, Y, DNA Methylation, Karyotyping, CpG Islands

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