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

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.

Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome‐wide polymorphic data

“…All barcoded raw reads were mapped to the P. lilfordi genome (rPodLil1.1, available at https://denovo.cnag.cat/podarcis) (Gomez‐Garrido et al., 2023) using the Burrows–Wheeler Aligner (BWA) software (v2.1) to generate individual Binary Alignment Map (BAM) files. The genome corresponds to a single female individual sampled in the Aire population (the population was included in our dataset).…”

“…The candidate SNP outliers were annotated by cross‐referencing the SNP position against the GFF file of the rPodLil1.1 genome assembly (Gomez‐Garrido et al., 2023) for Gene ID association. For outliers falling in protein‐coding region, a gene ontology (GO) annotation was performed, followed by a functional enrichment analysis with gGOSt in g:Profiler [https://biit.cs.ut.ee/gprofiler/gost] on individual datasets (GBS and RAD‐Seq).…”

“…A recent study based on single‐nucleotide polymorphisms (SNPs) data by restriction site‐associated DNA sequencing (RAD‐Seq) (Bassitta et al., 2021) has expanded on previous knowledge on genetic diversity and phylogeographic pattern of this species, confirming the existence of two well‐discriminated genetic lineages separating populations from the major archipelagos of Menorca and Mallorca/Cabrera (Brown et al., 2008; Terrasa et al., 2009). Recently, the P. lilfordi genome has been sequenced (Gomez‐Garrido et al., 2023) providing the framework for a comprehensive exploration of population‐level genomics of this species.…”

The BioGenome Portal: a web-based platform for biodiversity genomics data management

“…As of December 2023, the CBP instance contains a total of 58 organisms (Figure 4), five of them with already published assemblies (12)(13)(14)(15)(16). One of the unique features tailored for this instance is the integration of region-specific taxonomic information, focusing on the biodiversity found in Catalonia.…”

Efficient and Highly Continuous Chromosome-Level Genome Assembly of the First Chameleon Genome

“…However, compared with other amniote groups such as mammals and birds, squamate reptiles are lagging behind in terms of available reference genomes ( Hotaling et al 2021 ). Although new genomes are quickly emerging ( Bishop et al 2023 ; Gomez-Garrido et al 2023 ; Richmond et al 2023 ), there are still <100 genomes publicly available for the ∼11,549 squamate species ( Uetz et al 2021 ; Pinto et al 2023 ).…”