Y chromosome sequence and epigenomic reconstruction across human populations

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 seq...

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Autores: Esteller-Cucala, Paula|||0000-0003-3048-4280, Palmada-Flores, Marc|||0000-0003-0246-5226, Kuderna, Lukas F. K.|||0000-0002-9992-9295, Fontsere, Claudia|||0000-0003-2233-6026, Serres-Armero, Aitor|||0000-0003-1679-811X, Dabad, Marc|||0000-0002-6094-747X, Torralvo, María|||0000-0003-2267-1406, Faella, Armida|||0000-0001-8030-3092, Ferrández-Peral, Luis|||0000-0003-0338-0603, Llovera, Laia|||0000-0002-5836-593X, Fornas, Òscar|||0000-0003-2017-9100, Julià, Eva|||0000-0002-9722-4662, Ramírez, Erika, González, Irene, Hecht, Jochen, Lizano, Esther|||0000-0003-3304-9807, Juan, David|||0000-0003-1912-9667, Marquès i Bonet, Tomàs|||0000-0002-5597-3075
Formato: artículo
Fecha de publicación:2023
País:España
Recursos:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:279373
Acesso em linha:https://ddd.uab.cat/record/279373
https://dx.doi.org/urn:doi:10.1038/s42003-023-05004-9
Access Level:acceso abierto
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spelling Y chromosome sequence and epigenomic reconstruction across human populationsEsteller-Cucala, Paula|||0000-0003-3048-4280Palmada-Flores, Marc|||0000-0003-0246-5226Kuderna, Lukas F. K.|||0000-0002-9992-9295Fontsere, Claudia|||0000-0003-2233-6026Serres-Armero, Aitor|||0000-0003-1679-811XDabad, Marc|||0000-0002-6094-747XTorralvo, María|||0000-0003-2267-1406Faella, Armida|||0000-0001-8030-3092Ferrández-Peral, Luis|||0000-0003-0338-0603Llovera, Laia|||0000-0002-5836-593XFornas, Òscar|||0000-0003-2017-9100Julià, Eva|||0000-0002-9722-4662Ramírez, ErikaGonzález, IreneHecht, JochenLizano, Esther|||0000-0003-3304-9807Juan, David|||0000-0003-1912-9667Marquès i Bonet, Tomàs|||0000-0002-5597-3075Recent 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. 22023-01-0120232023-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/279373https://dx.doi.org/urn:doi:10.1038/s42003-023-05004-9reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengEuropean Commission https://doi.org/10.13039/501100000780 864203Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 PID2021-126004NB-100Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2021/SGR-00177open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2793732026-06-06T12:50:31Z
dc.title.none.fl_str_mv Y chromosome sequence and epigenomic reconstruction across human populations
title Y chromosome sequence and epigenomic reconstruction across human populations
spellingShingle Y chromosome sequence and epigenomic reconstruction across human populations
Esteller-Cucala, Paula|||0000-0003-3048-4280
title_short Y chromosome sequence and epigenomic reconstruction across human populations
title_full Y chromosome sequence and epigenomic reconstruction across human populations
title_fullStr Y chromosome sequence and epigenomic reconstruction across human populations
title_full_unstemmed Y chromosome sequence and epigenomic reconstruction across human populations
title_sort Y chromosome sequence and epigenomic reconstruction across human populations
dc.creator.none.fl_str_mv Esteller-Cucala, Paula|||0000-0003-3048-4280
Palmada-Flores, Marc|||0000-0003-0246-5226
Kuderna, Lukas F. K.|||0000-0002-9992-9295
Fontsere, Claudia|||0000-0003-2233-6026
Serres-Armero, Aitor|||0000-0003-1679-811X
Dabad, Marc|||0000-0002-6094-747X
Torralvo, María|||0000-0003-2267-1406
Faella, Armida|||0000-0001-8030-3092
Ferrández-Peral, Luis|||0000-0003-0338-0603
Llovera, Laia|||0000-0002-5836-593X
Fornas, Òscar|||0000-0003-2017-9100
Julià, Eva|||0000-0002-9722-4662
Ramírez, Erika
González, Irene
Hecht, Jochen
Lizano, Esther|||0000-0003-3304-9807
Juan, David|||0000-0003-1912-9667
Marquès i Bonet, Tomàs|||0000-0002-5597-3075
author Esteller-Cucala, Paula|||0000-0003-3048-4280
author_facet Esteller-Cucala, Paula|||0000-0003-3048-4280
Palmada-Flores, Marc|||0000-0003-0246-5226
Kuderna, Lukas F. K.|||0000-0002-9992-9295
Fontsere, Claudia|||0000-0003-2233-6026
Serres-Armero, Aitor|||0000-0003-1679-811X
Dabad, Marc|||0000-0002-6094-747X
Torralvo, María|||0000-0003-2267-1406
Faella, Armida|||0000-0001-8030-3092
Ferrández-Peral, Luis|||0000-0003-0338-0603
Llovera, Laia|||0000-0002-5836-593X
Fornas, Òscar|||0000-0003-2017-9100
Julià, Eva|||0000-0002-9722-4662
Ramírez, Erika
González, Irene
Hecht, Jochen
Lizano, Esther|||0000-0003-3304-9807
Juan, David|||0000-0003-1912-9667
Marquès i Bonet, Tomàs|||0000-0002-5597-3075
author_role author
author2 Palmada-Flores, Marc|||0000-0003-0246-5226
Kuderna, Lukas F. K.|||0000-0002-9992-9295
Fontsere, Claudia|||0000-0003-2233-6026
Serres-Armero, Aitor|||0000-0003-1679-811X
Dabad, Marc|||0000-0002-6094-747X
Torralvo, María|||0000-0003-2267-1406
Faella, Armida|||0000-0001-8030-3092
Ferrández-Peral, Luis|||0000-0003-0338-0603
Llovera, Laia|||0000-0002-5836-593X
Fornas, Òscar|||0000-0003-2017-9100
Julià, Eva|||0000-0002-9722-4662
Ramírez, Erika
González, Irene
Hecht, Jochen
Lizano, Esther|||0000-0003-3304-9807
Juan, David|||0000-0003-1912-9667
Marquès i Bonet, Tomàs|||0000-0002-5597-3075
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
description 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.
publishDate 2023
dc.date.none.fl_str_mv 2
2023-01-01
2023
2023-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/279373
https://dx.doi.org/urn:doi:10.1038/s42003-023-05004-9
url https://ddd.uab.cat/record/279373
https://dx.doi.org/urn:doi:10.1038/s42003-023-05004-9
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv European Commission https://doi.org/10.13039/501100000780 864203
Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 PID2021-126004NB-100
Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2021/SGR-00177
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
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repository.mail.fl_str_mv
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