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Nat Commun
2017 Nov 10;81:1433. doi: 10.1038/s41467-017-01316-7.
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The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.
Hammond SA
,
Warren RL
,
Vandervalk BP
,
Kucuk E
,
Khan H
,
Gibb EA
,
Pandoh P
,
Kirk H
,
Zhao Y
,
Jones M
,
Mungall AJ
,
Coope R
,
Pleasance S
,
Moore RA
,
Holt RA
,
Round JM
,
Ohora S
,
Walle BV
,
Veldhoen N
,
Helbing CC
,
Birol I
.
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Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. 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. We report a 5.8 Gbp (NG50 = 69 kbp) genome assembly of a representative North American bullfrog (Rana [Lithobates] catesbeiana). The genome contains over 22,000 predicted protein-coding genes and 6,223 candidate long noncoding RNAs (lncRNAs). RNA-Seq experiments show thyroid hormone causes widespread transcriptional change among protein-coding and putative lncRNA genes. This initial bullfrog draft genome will serve as a key resource with broad utility including amphibian research, developmental biology, and environmental research.
Fig. 1. Median DESeq2-normalized counts of genes detected in the back skin of premetamorphic Rana catesbeiana tadpoles treated with vehicle control or T3 for 48 h. Gene transcripts determined to be significantly differentially expressed (DESeq2 adjusted p-value < 0.05) are indicated in pink, while the remainder are semi-transparent black to convey density. Both predicted protein coding and putative lncRNA genes are depicted
Fig. 2. Molecular phylogenetic analysis of amphibian mitochondrial genomes and genes. The phylogenetic tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved a complete mitochondrial (Mt) genome sequences of salamanders, toads and frogs, classified as Rana (blue highlight) or Lithobates (yellow highlight). Analysis of Mt genes b
cyb, c
rnr1, and d
rnr2 of selected frog species. Position of R. catesbeiana indicated by an asterisk
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