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

Lukas F. K. Kuderna (), Esther Lizano (), Eva Julià, Jessica Gomez-Garrido, Aitor Serres-Armero, Martin Kuhlwilm, Regina Antoni Alandes, Marina Alvarez-Estape, David Juan, Heath Simon, Tyler Alioto, Marta Gut, Ivo Gut, Mikkel Heide Schierup, Oscar Fornas and Tomas Marques-Bonet ()
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Lukas F. K. Kuderna: PRBB
Esther Lizano: PRBB
Eva Julià: Institut Hospital del Mar d’Investigacions Mèdiques (IMIM)
Jessica Gomez-Garrido: The Barcelona Institute of Science and Technology
Aitor Serres-Armero: PRBB
Martin Kuhlwilm: PRBB
Regina Antoni Alandes: The Barcelona Institute of Science and Technology
Marina Alvarez-Estape: PRBB
David Juan: PRBB
Heath Simon: The Barcelona Institute of Science and Technology
Tyler Alioto: The Barcelona Institute of Science and Technology
Marta Gut: The Barcelona Institute of Science and Technology
Ivo Gut: The Barcelona Institute of Science and Technology
Mikkel Heide Schierup: Aarhus University
Oscar Fornas: The Barcelona Institute for Science and Technology
Tomas Marques-Bonet: PRBB

Nature Communications, 2019, vol. 10, issue 1, 1-8

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-018-07885-5

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