Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

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

Gomez-Garrido, Jessica ; Cruz, Fernando ; Alioto, Tyler S. ; Feiner, Nathalie LU ; Uller, Tobias LU ; Gut, Marta ; Sanchez Escudero, Ignacio ; Tavecchia, Giacomo ; Rotger, Andreu and Otalora Acevedo, Katherin Eliana , et al. (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)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and , et al. (More)
; ; ; ; ; ; ; ; ; and (Less)
organization
publishing date
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
  • pmid:37137526
  • scopus:85161312292
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
2024-04-20 01:10:13
@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 &gt;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}},
}