Genome Annotation of the Genetic Model, Xenopus laevis, Enriched for the Developing Central Nervous System

Xenopus laevis is a valuable genetic model system for the study of brain development and neuroregeneration. A significant limitation to high throughput gene expression studies in this model has been a shortage of well-annotated genome based on deep transcriptomic sequencing. While initial genomic efforts focused primarily on the eudiploid sister species, X. tropicalis, genome sequencing of X. laevis has recently advanced to cover over 89% of the allotetraploid genome with a first generation annotation based primarily on predictive gene models. The brain is known to have a high ratio of isoforms/genes. Our goal is to create a comprehensive profile of the transcriptomes in the developing X. laevis tadpole brain.

We are updating the annotatation of the X. laevis genome (build 7.2) based on three sources. First, de novo assembly of 197 Gbp of RNA-Seq deep transcriptome sequence using Trinity. Specifically, we carried out RNA-Seq analysis of forebrain, midbrain, and hindbrain tissues from tadpoles stages 46 and 49, together with adult brain, skin, heart, lung, skeletal muscle, liver, and fat. Second, we are incorporating over 600 Mbp of full length cDNA, ESTs, and other transcribed X. laevis sequences available from the public databases using PASA. Third, genome-guided assembly (build 7.2, Trinity & GSNAP) is being used to further improve the reannotation. We anticipate that an updated annotation of the X. laevis genome, including data of alternate splice variants, addition of UTR sequences, and noncoding RNAs will provide an essential resource for the Xenopus community and for cross species genome analysis.