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Download fileGenotyping-by-Sequencing (GBS) of large amphibian genomes: a comparative study of two non-model species endemic to Italy: supplementary material
journal contribution
posted on 2019-01-02, 11:48 authored by Valentina Rovelli, Aritz Ruiz-González, Leonardo Vignoli, Daniele Macale, Vincenzo Buono, Francesca Davoli, David R. Vieites, Nadav Pezaro, Ettore RandiNext Generation
Sequencing (NGS) and related technologies have revolutionized the field of conservation
and population genetics, providing novel tools and the capacity to discover
thousands of new Single Nucleotide Polymorphisms (SNPs) for the analysis of
population parameters. However, gathering NGS data for organisms with very
large genomes, such as amphibians, remains challenging because it is still
unclear how the current methods perform. Here, we use the Genotyping-by-Sequencing
(GBS) approach to generate SNP data for the genotyping of two amphibian species
that are of conservation concern, the Sardinian brook salamander (Euproctus platycephalus) and the Italian
stream frog (Rana italica). Both E. platycephalus and R. italica have very large genomes (5.53
Gb and >20 Gb, respectively) so genomic data are not available for either of
them. We used 95 individual samples and one Illumina lane for each species, with
an additional lane for E. platycephalus.
After filtering, we obtained 961 and 854 high-coverage SNPs for E. platycephalus and R. italica, respectively. Our results
suggest that GBS can serve as a reliable and cost-effective method for
genotyping large amphibian genomes, including non-model species.