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Tytuł:
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Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).
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Autorzy:
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Gomez-Garrido J; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.
Cruz F; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.
Alioto TS; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.
Feiner N; Department of Biology, Lund University, Lund, Sweden.
Uller T; Department of Biology, Lund University, Lund, Sweden.
Gut M; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Sanchez Escudero I; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.
Tavecchia G; Animal Demography and Ecology Unit, IMEDEA, CSIC-UIB, Esporles, Spain.
Rotger A; Animal Demography and Ecology Unit, IMEDEA, CSIC-UIB, Esporles, Spain.
Otalora Acevedo KE; Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain.; Fundación Motiva Inteligencia Colectiva, Biodiversity Branch, Tunja, Boyacá, Colombia.
Baldo L; Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain.; Institute for Research on Biodiversity (IRBio), University of Barcelona, Barcelona, Spain.
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Źródło:
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DNA research : an international journal for rapid publication of reports on genes and genomes [DNA Res] 2023 Jun 01; Vol. 30 (3).
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Typ publikacji:
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Journal Article
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Język:
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English
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Imprint Name(s):
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Publication: 2006- : Oxford : Oxford University Press
Original Publication: Tokyo, Japan : Kazusa DNA Research Institute ; Universal Academy Press [1994-
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MeSH Terms:
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Chromosomes*
Lizards*/genetics
Animals ; Spain ; Molecular Sequence Annotation ; Genome
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Grant Information:
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PRO2020-S02 Catalan Initiative for the Earth Biogenome Project; VR 2017-03846 Swedish Research Council; 948126 Starting Grant from the European Research Council
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Contributed Indexing:
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Keywords: Hi-C; Oxford Nanopore Technologies (ONT); RNAseq; mitochondrial genome; reptile
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Entry Date(s):
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Date Created: 20230503 Date Completed: 20230601 Latest Revision: 20230601
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Update Code:
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20240105
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PubMed Central ID:
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PMC10214862
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DOI:
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10.1093/dnares/dsad008
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PMID:
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37137526
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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.
(© The Author(s) 2023. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.)
