Genotyping-by-Sequencing (GBS) of large amphibian genomes: a comparative study of two non-model species endemic to Italy: supplementary material
Valentina Rovelli
Aritz Ruiz-González
Leonardo Vignoli
Daniele Macale
Vincenzo Buono
Francesca Davoli
David R. Vieites
Nadav Pezaro
Ettore Randi
10.6084/m9.figshare.7392227.v1
https://brill.figshare.com/articles/journal_contribution/Genotyping-by-Sequencing_GBS_of_large_amphibian_genomes_a_comparative_study_of_two_non-model_species_endemic_to_Italy_supplementary_material/7392227
Next 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 (<i>Euproctus platycephalus</i>) and the Italian
stream frog (<i>Rana italica</i>). Both <i>E. platycephalus</i> and <i>R. italica</i> 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 <i>E. platycephalus</i>.
After filtering, we obtained 961 and 854 high-coverage SNPs for <i>E. platycephalus</i> and <i>R. italica</i>, respectively. Our results
suggest that GBS can serve as a reliable and cost-effective method for
genotyping large amphibian genomes, including non-model species.
2019-01-02 11:48:52
conservation genomics
frog
newt
Next Generation Sequencing
SNPs
whole genome duplications
Ecology not elsewhere classified