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Author: S Austin Hammond
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Research area: genomics
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It′s okay to be green: Draft genome of the North American Bullfrog (Rana [Lithobates] catesbeiana)


Created on 18th January 2017

S Austin Hammond; René L Warren; Benjamin P Vandervalk; Erdi Kucuk; Hamza Khan; Ewan A Gibb; Pawan Pandoh; Heather Kirk; Yongjun Zhao; Martin Jones; Andrew J Mungall; Robin Coope; Stephen Pleasance; Richard A Moore; Robert A Holt; Jessica M Round; Sara Ohora; Nik Veldhoen; Caren C Helbing; Inanc Birol;


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 frogs Xenopus tropicalis and Xenopus laevis. 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. Herein, 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 (88-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 de novo assembler Kollector and Illumina TruSeq, 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 more than 6,000 candidate long noncoding RNAs (lncRNAs) from a composite reference bullfrog transcriptome. Mitochondrial sequence analysis supports the phylogenetic positioning of the bullfrog within the genus Rana rather than Lithobates. Our draft bullfrog genome will serve as a useful resource for the amphibian research community and we demonstrate its utility in RNA-seq experiments to identify differential gene expression in the back skin of premetamorphic tadpoles subjected to thyroid hormone treatment.

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