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Y chromosome sequence and epigenomic reconstruction across human populations

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dc.contributor.author Esteller Cucala, Paula
dc.contributor.author Palmada Flores, Marc
dc.contributor.author Kuderna, Lukas F.K.
dc.contributor.author Fontseré Alemany, Clàudia, 1992-
dc.contributor.author Serres Armero, Aitor, 1992-
dc.contributor.author Dabad, Marc
dc.contributor.author Torralvo, María
dc.contributor.author Faella, Armida
dc.contributor.author Ferrández Peral, Luis, 1991-
dc.contributor.author Llovera Nadal, Laia
dc.contributor.author Fornas Carreño, Oscar
dc.contributor.author Julià, Eva
dc.contributor.author Ramírez, Erika
dc.contributor.author González, Irene
dc.contributor.author Hecht, Jochen
dc.contributor.author Lizano González, Esther, 1974-
dc.contributor.author Juan, David
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.date.accessioned 2023-09-13T07:12:38Z
dc.date.available 2023-09-13T07:12:38Z
dc.date.issued 2023
dc.identifier.citation Esteller-Cucala P, Palmada-Flores M, Kuderna LFK, Fontsere C, Serres-Armero A, Dabad M, Torralvo M, Faella A, Ferrández-Peral L, Llovera L, Fornas O, Julià E, Ramírez E, González I, Hecht J, Lizano E, Juan D, Marquès-Bonet T. Y chromosome sequence and epigenomic reconstruction across human populations. Commun Biol. 2023;6:623. DOI: 10.1038/s42003-023-05004-9
dc.identifier.issn 2399-3642
dc.identifier.uri http://hdl.handle.net/10230/57856
dc.description.abstract Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications among the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.
dc.description.sponsorship M.P.-F. has the support of an INPhINIT Retaining Fellowship from “La Caixa” Foundation (ID 100010434) with code LCF/BQ/DR20/11790032. T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), PID2021-126004NB-100 (MICIIN/FEDER, UE) and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2021 SGR 00177).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Nature Research
dc.relation.ispartof Commun Biol. 2023;6:623
dc.rights © The Author(s) 2023. 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/
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Y chromosome sequence and epigenomic reconstruction across human populations
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/s42003-023-05004-9
dc.subject.keyword Comparative genomics
dc.subject.keyword Epigenomics
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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