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

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Title:	Selective single molecule sequencing and assembly of a human Y chromosome of African origin
Author:	Kuderna, Lukas F.K.; Lizano, Esther; Julià, Eva; Gómez Garrido, Jèssica; Serres Armero, Aitor; Kuhlwilm, Martin; Alandes, Regina Antoni; Alvarez-Estape, Marina; Juan, David; Simon, Heath; Alioto, Tyler; Gut, Marta; Gut, Ivo Glynne; Schierup, Mikkel H.; Fornas Carreño, Oscar; Marquès i Bonet, Tomàs, 1975-
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.
Abstract:	This study was supported by the Spanish Ministry of Economy and Competitiveness with Proyectos de I+D “Excelencia” y Proyectos de I+D+I “Retos Investigación” BFU2014-55090-P awarded to T.M.-B. and O.F., Centro de Excelencia Severo Ochoa 2013–2017 and Centro de Excelencia Maria de Maeztu 2016–2019. We acknowledge the support from the CERCA Programme of the Generalitat de Catalunya, institutional support from the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) through the Instituto de Salud Carlos III, from the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement, and co-financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014–2020 Smart Growth Operating Program. L.F.K.K. is supported by an FPI fellowship associated with BFU2014-55090-P (MINECO/FEDER, UE). M.K. is supported by a Deutsche Forschungsgemeinschaft (DFG) fellowship (KU 3467/1-1). T.M.-B. is supported by BFU2017-86471-P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya. D.J. is supported by a Juan de la Cierva fellowship (FJCI-2016-29558) from MICINN.
Subject(s):	-Comparative genomics -Genome assembly algorithms -Genomics
Rights:	© The Author(s) 2019. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. http://creativecommons.org/licenses/by/4.0/
Document type:	Article Article - Published version
Published by:	Nature Research
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