Selective single molecule sequencing and assembly of a human Y chromosome of African origin
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.
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Format: | artículo biblioteca |
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Springer Nature
2019-01-02
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Subjects: | Comparative genomics, Genome assembly algorithms, Genomics, |
Online Access: | http://hdl.handle.net/10261/207209 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100004587 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100001659 |
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dig-ibe-es-10261-2072092021-12-27T16:01:51Z Selective single molecule sequencing and assembly of a human Y chromosome of African origin 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 S. Gut, Marta Gut, Ivo Schierup, Mikkel Heide Fornas, Oscar Marqués-Bonet, Tomàs Ministerio de Economía y Competitividad (España) Generalitat de Catalunya Instituto de Salud Carlos III European Commission German Research Foundation Comparative genomics Genome assembly algorithms Genomics 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. 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. 2020-04-13T07:54:32Z 2020-04-13T07:54:32Z 2019-01-02 2020-04-13T07:54:32Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1038/s41467-018-07885-5 e-issn: 2041-1723 Nature Communications 10: 4 (2019) http://hdl.handle.net/10261/207209 10.1038/s41467-018-07885-5 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100004587 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100001659 30602775 #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2014-55090-P info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/BFU2017-86471-P info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/FJCI-2016-29558 Publisher's version http://doi.org/10.1038/s41467-018-07885-5 Sí open Springer Nature |
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Comparative genomics Genome assembly algorithms Genomics Comparative genomics Genome assembly algorithms Genomics |
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Comparative genomics Genome assembly algorithms Genomics Comparative genomics Genome assembly algorithms Genomics 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 S. Gut, Marta Gut, Ivo Schierup, Mikkel Heide Fornas, Oscar Marqués-Bonet, Tomàs Selective single molecule sequencing and assembly of a human Y chromosome of African origin |
description |
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. |
author2 |
Ministerio de Economía y Competitividad (España) |
author_facet |
Ministerio de Economía y Competitividad (España) 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 S. Gut, Marta Gut, Ivo Schierup, Mikkel Heide Fornas, Oscar Marqués-Bonet, Tomàs |
format |
artículo |
topic_facet |
Comparative genomics Genome assembly algorithms Genomics |
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 S. Gut, Marta Gut, Ivo Schierup, Mikkel Heide Fornas, Oscar Marqués-Bonet, Tomàs |
author_sort |
Kuderna, Lukas F. K. |
title |
Selective single molecule sequencing and assembly of a human Y chromosome of African origin |
title_short |
Selective single molecule sequencing and assembly of a human Y chromosome of African origin |
title_full |
Selective single molecule sequencing and assembly of a human Y chromosome of African origin |
title_fullStr |
Selective single molecule sequencing and assembly of a human Y chromosome of African origin |
title_full_unstemmed |
Selective single molecule sequencing and assembly of a human Y chromosome of African origin |
title_sort |
selective single molecule sequencing and assembly of a human y chromosome of african origin |
publisher |
Springer Nature |
publishDate |
2019-01-02 |
url |
http://hdl.handle.net/10261/207209 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100004587 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100001659 |
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