Genome assembly of the endangered Santa Marta Harlequin Toad, Atelopus laetissimus, endemic to the Sierra Nevada de Santa Marta of Colombia

Abstract Despite the critical conservation status of many harlequin toads (Anura: Bufonidae: Atelopus) and their significance in elucidating the impacts of emerging diseases on amphibians, genomic data for this genus are scarce. Here, we present a de novo genome assembly of the Santa Marta Harlequin Toad, Atelopus laetissimus, using PacBio HiFi sequencing data, representing the first published Atelopus genome assembly and only the second amphibian genome assembly from Colombia. The assembly consists of 1,487 contigs at 35X coverage with an N50 of 31 Mb and a total length of 3.5 Gb. A Tetrapoda BUSCO score of 92% suggests our assembly is very nearly complete. Analysis revealed a high repeat content, with 70% of the genome consisting of interspersed repeats. This high-contiguity draft assembly will drive the search for a possible genetic basis of pathogen resistance in these endangered toads of the Sierra Nevada de Santa Marta, as well as facilitate ongoing evolutionary studies.