Esteller Cucala, PaulaPalmada Flores, MarcKuderna, Lukas, 1989-Fontseré Alemany, Clàudia, 1992-Serres Armero, Aitor, 1992-Dabad, MarcTorralvo, MaríaFaella, ArmidaFerrández Peral, Luis, 1991-Llovera Nadal, LaiaFornas Carreño, OscarJulià, EvaRamírez, ErikaGonzález, IreneHecht, JochenLizano González, Esther, 1974-Juan, DavidMarquès i Bonet, Tomàs, 1975-2023-09-132023-09-132023Esteller-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/s42003-023-05004-92399-3642http://hdl.handle.net/10230/57856Recent 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.application/pdfeng© 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/info:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/s42003-023-05004-9Comparative genomicsEpigenomicsinfo:eu-repo/semantics/openAccess