North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA
In a recent Nature Communications publication, Hammond et al., report on sequencing, assembly and annotation of the draft North American bullfrog genome. The researchers used some the latest sequencing and bioinformatics technologies, including 10x Linked-Reads and the ARCs (Assembly Round-up by Chromium Scaffolding) application for genome scaffolding.
ABSTRACT
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.
Read the full article in Nature Communications.
Read more about scaffolding genome drafts with ARCs and Linked-Reads.
Linked-Read Resources
- Learn more about the Chromium™ de novo Solution
- See the latest Linked-Read assembly publications
- Read the blog post Everything you wanted to know about Linked-Reads