Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)

The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management p...

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Autores: Gómez Garrido, Jèssica, Cruz, Fernando, Alioto, Tyler, Feiner, Nathalie, Uller, Tobias, Sanchez Escudero, Ignacio, Tavecchia, Giacomo, Rotger, Andreu, Otalora Acevedo, Katherin Eliana, Baldo, Laura
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/57595
Acceso en línea:http://hdl.handle.net/10230/57595
http://dx.doi.org/10.1093/dnares/dsad008
Access Level:acceso abierto
Palabra clave:Hi-C
Oxford Nanopore Technologies (ONT)
RNAseq
Mitochondrial genome
Reptile
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network_acronym_str ES
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spelling Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)Gómez Garrido, JèssicaCruz, FernandoAlioto, TylerFeiner, NathalieUller, TobiasSanchez Escudero, IgnacioTavecchia, GiacomoRotger, AndreuOtalora Acevedo, Katherin ElianaBaldo, LauraHi-COxford Nanopore Technologies (ONT)RNAseqMitochondrial genomeReptileThe Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.This study was supported by the Institut d’Estudis Catalans under the Catalan Initiative for the Earth Biogenome Project (PRO2020-S02 to L.B.), the Swedish Research Council (VR 2017-03846 and VR-2021-04656 to T.U. and VR-2020-03650 to N.F.) and Starting Grant from the European Research Council (no. 948126 to N.F.). We also acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme/Generalitat de Catalunya, the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement. Co-financing funds were obtained from the European Regional Development Fund by the Spanish Ministry of Science and Innovation corresponding to the Programa Operativo FEDER Plurirregional de España (POPE) 2014-2020 and by the Secretaria d’Universitats i Recerca, Departament d’Empresa i Coneixement of the Generalitat de Catalunya corresponding to the Programa Operatiu FEDER de Catalunya 2014-2020.Oxford University Press202320232023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/57595http://dx.doi.org/10.1093/dnares/dsad008reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésDNA Res. 2023 Jun 1;30(3):dsad008info:eu-repo/grantAgreement/EC/H2020/948126© The Author(s) 2023. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/575952026-05-29T05:05:01Z
dc.title.none.fl_str_mv Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
title Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
spellingShingle Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
Gómez Garrido, Jèssica
Hi-C
Oxford Nanopore Technologies (ONT)
RNAseq
Mitochondrial genome
Reptile
title_short Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
title_full Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
title_fullStr Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
title_full_unstemmed Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
title_sort Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
dc.creator.none.fl_str_mv Gómez Garrido, Jèssica
Cruz, Fernando
Alioto, Tyler
Feiner, Nathalie
Uller, Tobias
Sanchez Escudero, Ignacio
Tavecchia, Giacomo
Rotger, Andreu
Otalora Acevedo, Katherin Eliana
Baldo, Laura
author Gómez Garrido, Jèssica
author_facet Gómez Garrido, Jèssica
Cruz, Fernando
Alioto, Tyler
Feiner, Nathalie
Uller, Tobias
Sanchez Escudero, Ignacio
Tavecchia, Giacomo
Rotger, Andreu
Otalora Acevedo, Katherin Eliana
Baldo, Laura
author_role author
author2 Cruz, Fernando
Alioto, Tyler
Feiner, Nathalie
Uller, Tobias
Sanchez Escudero, Ignacio
Tavecchia, Giacomo
Rotger, Andreu
Otalora Acevedo, Katherin Eliana
Baldo, Laura
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Hi-C
Oxford Nanopore Technologies (ONT)
RNAseq
Mitochondrial genome
Reptile
topic Hi-C
Oxford Nanopore Technologies (ONT)
RNAseq
Mitochondrial genome
Reptile
description The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/57595
http://dx.doi.org/10.1093/dnares/dsad008
url http://hdl.handle.net/10230/57595
http://dx.doi.org/10.1093/dnares/dsad008
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv DNA Res. 2023 Jun 1;30(3):dsad008
info:eu-repo/grantAgreement/EC/H2020/948126
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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