Welcome to the UPF Digital Repository

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

Show simple item record

dc.contributor.author Gómez-Garrido, Jèssica
dc.contributor.author Cruz, Fernando
dc.contributor.author Alioto, Tyler
dc.contributor.author Feiner, Nathalie
dc.contributor.author Uller, Tobias
dc.contributor.author Gut, Marta
dc.contributor.author Sanchez Escudero, Ignacio
dc.contributor.author Tavecchia, Giacomo
dc.contributor.author Rotger, Andreu
dc.contributor.author Otalora Acevedo, Katherin Eliana
dc.contributor.author Baldo, Laura
dc.date.accessioned 2023-09-13T07:12:42Z
dc.date.available 2023-09-13T07:12:42Z
dc.date.issued 2023
dc.identifier.citation Gomez-Garrido J, Cruz F, Alioto TS, Feiner N, Uller T, Gut M, Sanchez Escudero I, Tavecchia G, Rotger R, Otalora Acevedo KE, Baldo L. Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). DNA Res. 2023;30(3):dsad008. DOI: 10.1093/dnares/dsad008
dc.identifier.issn 1340-2838
dc.identifier.uri http://hdl.handle.net/10230/57857
dc.description.abstract 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.
dc.description.sponsorship 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.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof DNA Res. 2023;30(3):dsad008
dc.rights © The Author(s) 2023. 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.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/dnares/dsad008
dc.subject.keyword Hi-C
dc.subject.keyword Oxford Nanopore Technologies (ONT)
dc.subject.keyword RNAseq
dc.subject.keyword Mitochondrial genome
dc.subject.keyword Reptile
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/948126
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


This item appears in the following Collection(s)

Show simple item record

Search DSpace

Advanced Search


My Account


In collaboration with Compliant to Partaking