It’s okay to be green: Draft genome of the North American Bullfrog (Rana [Lithobates] catesbeiana)

Hammond, S. A.; Warren, R. L.; Vandervalk, B. P.; Kucuk, E.; Khan, H.; Gibb, E. A.; Pandoh, P.; Kirk, H.; Zhao, Y.; Jones, M.; Mungall, A. J.; Coope, R.; Pleasance, S.; Moore, R. A.; Holt, R. A.; Round, J. M.; Ohora, S.; Veldhoen, N.; Helbing, C. C.; Birol, I.

doi:10.1101/100149

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bioRxiv · 10.1101/100149

It’s okay to be green: Draft genome of the North American Bullfrog (Rana [Lithobates] catesbeiana)

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Abstract

Frogs play important ecological roles as sentinels, insect control and food sources. Several species are important model organisms for scientific research to study embryogenesis, development, immune function, and endocrine signaling. The globally-distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Consequently, the extensive Xenopus genomic resources are of limited utility for Ranids and related 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.\n\nHerein, we report on the first genome sequence of a Ranid species, an adult male North American bullfrog (Rana [Lithobates] catesbeiana). We assembled high-depth Illumina reads (66-fold coverage), into a 5.8 Gbp (NG50 = 57.7 kbp) draft genome using ABySS v1.9.0. The assembly was scaffolded with LINKS and RAILS using pseudo-long-reads from targeted denovo assembler Kollector and Illumina Synthetic Long-Reads, as well as reads from long fragment (MPET) libraries. We predicted over 22,000 protein-coding genes using the MAKER2 pipeline and identified the genomic loci of 6,227 candidate long noncoding RNAs (IncRNAs) from a composite reference bullfrog transcriptome. Mitochondrial sequence analysis supported Lithobates as a subgenus of Rana. RNA-Seq experiments identified ~6,000 thyroid hormone- responsive transcripts in the back skin of premetamorphic tadpoles; the majority of which regulate DNA/RNA processing. Moreover, 1/6th of differentially-expressed transcripts were putative lncRNAs. Our draft bullfrog genome will serve as a useful resource for the amphibian research community.

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Hammond, S. A., Warren, R. L., Vandervalk, B. P., Kucuk, E., Khan, H., Gibb, E. A., Pandoh, P., Kirk, H., Zhao, Y., Jones, M., Mungall, A. J., Coope, R., Pleasance, S., Moore, R. A., Holt, R. A., Round, J. M., Ohora, S., Veldhoen, N., Helbing, C. C., Birol, I.. 2017-01-13. It’s okay to be green: Draft genome of the North American Bullfrog (Rana [Lithobates] catesbeiana). https://doi.org/10.1101/100149

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