Draft Genome of the North American Bullfrog (Rana [Lithobates] catesbeiana)

Frogs play important ecological roles, including insect control and as food sources, and several species are important model organisms for scientific research with aims to study embryogenesis, body development and endocrine signaling. The globally-distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory frogs Xenopus tropicalis and Xenopus laevis. Consequently, the extensive Xenopus genomic resources are of limited utility to studying Ranids and other frog species. More widely-applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines.

Here, we report on the first genome sequence of a Ranid species, an adult male North American bullfrog. We assembled high-depth Illumina reads (88-fold coverage), into a 5.8 Gbp (NG50 = 57.7 kbp) draft genome using ABySS v1.9.0. The assembly is scaffolded with LINKS and RAILS using pseudo-long-reads from targeted de novo assembler Kollector and Illumina TruSeq, as well as reads from long fragment (MPET) libraries. Our assembly indicates that the bullfrog genome is more than three times larger than the X. tropicalis genome, and almost twice as large as that of X. laevis. We predicted over 22 thousand protein-coding genes using the MAKER2 pipeline and identified the genomic loci of more than 6 thousand candidate long noncoding RNAs (lncRNAs) from a composite reference bullfrog transcriptome. Our draft bullfrog genome will serve as a useful resource for the amphibian research community, and will facilitate large-scale genomic analyses and comparative genomic experiments.