RT Journal Article
SR Electronic
T1 It’s okay to be green: Draft genome of the North American bullfrog (Rana [Lithobates] catesbeiana)
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 100149
DO 10.1101/100149
A1 S. Austin Hammond
A1 René L. Warren
A1 Benjamin P. Vandervalk
A1 Erdi Kucuk
A1 Hamza Khan
A1 Ewann A. Gibb
A1 Pawan Pandoh
A1 Heather Kirk
A1 Yongjun Zaho
A1 Martin Jones
A1 Andrew J. Mungall
A1 Robin Coope
A1 Stephen Pleasance
A1 Richard A. Moore
A1 Robert A. Holt
A1 Jessica M. Round
A1 Sara Ohora
A1 Branden V. Walle
A1 Nik Veldhoen
A1 Caren C. Helbing
A1 Inanc Birol
YR 2017
UL http://biorxiv.org/content/early/2017/02/02/100149.abstract
AB 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.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 (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.