Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)
(2023) In DNA Research 30(3).- 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... (More)
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.
(Less)
- author
- organization
- publishing date
- 2023
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Hi-C, mitochondrial genome, Oxford Nanopore Technologies (ONT), reptile, RNAseq
- in
- DNA Research
- volume
- 30
- issue
- 3
- article number
- dsad008
- publisher
- Oxford University Press
- external identifiers
-
- scopus:85161312292
- pmid:37137526
- ISSN
- 1340-2838
- DOI
- 10.1093/dnares/dsad008
- language
- English
- LU publication?
- yes
- id
- 4472f2ac-2ad1-4b96-b95f-e5109c1d74c7
- date added to LUP
- 2023-08-21 15:11:00
- date last changed
- 2024-06-15 06:19:16
@article{4472f2ac-2ad1-4b96-b95f-e5109c1d74c7, abstract = {{<p>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.</p>}}, author = {{Gomez-Garrido, Jessica and Cruz, Fernando and Alioto, Tyler S. and Feiner, Nathalie and Uller, Tobias and Gut, Marta and Sanchez Escudero, Ignacio and Tavecchia, Giacomo and Rotger, Andreu and Otalora Acevedo, Katherin Eliana and Baldo, Laura}}, issn = {{1340-2838}}, keywords = {{Hi-C; mitochondrial genome; Oxford Nanopore Technologies (ONT); reptile; RNAseq}}, language = {{eng}}, number = {{3}}, publisher = {{Oxford University Press}}, series = {{DNA Research}}, title = {{Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)}}, url = {{http://dx.doi.org/10.1093/dnares/dsad008}}, doi = {{10.1093/dnares/dsad008}}, volume = {{30}}, year = {{2023}}, }