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

Gomez-Garrido, Jessica (author)
Center for Genomic Regulation (CRG)
Cruz, Fernando (author)
Center for Genomic Regulation (CRG)
Alioto, Tyler S. (author)
Center for Genomic Regulation (CRG)
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Feiner, Nathalie (author)
Lund University,Lunds universitet,Evolutionär ekologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Evolutionsbiologi,Forskargrupper vid Lunds universitet,Evolutionary ecology,Department of Biology,Faculty of Science,Evolutionary Biology,Lund University Research Groups
Uller, Tobias (author)
Lund University,Lunds universitet,Evolutionär ekologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Evolutionsbiologi,Forskargrupper vid Lunds universitet,Evolutionary ecology,Department of Biology,Faculty of Science,Evolutionary Biology,Lund University Research Groups
Gut, Marta (author)
Pompeu Fabra University,Center for Genomic Regulation (CRG)
Sanchez Escudero, Ignacio (author)
Center for Genomic Regulation (CRG)
Tavecchia, Giacomo (author)
CSIC Spanish National Research Council
Rotger, Andreu (author)
CSIC Spanish National Research Council
Otalora Acevedo, Katherin Eliana (author)
University of Barcelona
Baldo, Laura (author)
University of Barcelona
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 (creator_code:org_t)
2023
2023
English.
In: DNA Research. - 1340-2838. ; 30:3
Related links:
http://dx.doi.org/10... (free)
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https://lup.lub.lu.s...
https://doi.org/10.1...
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  • Journal article (peer-reviewed)
Abstract Subject headings
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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.

Subject headings

NATURVETENSKAP  -- Biologi -- Evolutionsbiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Evolutionary Biology (hsv//eng)

Keyword

Hi-C
mitochondrial genome
Oxford Nanopore Technologies (ONT)
reptile
RNAseq

Publication and Content Type

art (subject category)
ref (subject category)

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