NewtBase

The Newtbase contains genomic resources obtained through transcriptome sequencing of the Lissotriton montandoni/vulgaris newts. Huge salamander genomes contain large amounts of repetitive sequences, therefore transcriptome sequencing is an efficient way of reducing complexity and obtaining genome-wide information. For more background about the evolutionary biology of the Lissotriton vulgaris/montandoni system see our publications

Paired-end (2 x 100 bp) Illumina RNASeq data were obtained from the liver of six L. montandoni and six L. vulgaris individuals (overall 362 mln reads, on average 30 mln reads per sample) and the spleen of two L. vulgaris individuals (108 mln reads). Transcriptome was de novo assembled using Trinity and redundancy of the Trinity assembly was reduced using the approach of Stuglik et al. 2014. Reads from both species were assembled together because sequence divergence between the two species is low and shared polymorphisms are abundant, both due to the relatively recent ancestry and due to ongoing hybridization. Transcriptome resources are available for blast-searching and download. The liver reference transcriptome obtained from a single Lissotriton helveticus individual, 9.8 mln reads is also available for download

In addition to the reference transcriptome we present a manually curated set of coding sequences of almost 800 genes involved in immune response.