A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology. (22nd April 2019)

• Record Type: Journal Article
• Authors: Matsunami, Masatoshi; Suzuki, Miyuki; Haramoto, Yoshikazu; Fukui, Akimasa; Inoue, Takeshi; Yamaguchi, Katsushi; Uchiyama, Ikuo; Mori, Kazuki; Tashiro, Kosuke; Ito, Yuzuru; Takeuchi, Takashi; Suzuki, Ken-ichi T; Agata, Kiyokazu; Shigenobu, Shuji; Hayashi, Toshinori
• Is Part Of: DNA research. Volume 26:Number 3(2019)
• Page Start: 217
• Page End: 229
• Publication Date: 2019-04-22
• Subjects: transcriptome -- Iberian ribbed newt -- NGS -- model organism; Genes -- Periodicals; Genomes -- Periodicals; Genes -- Research -- Periodicals; Genomics -- Periodicals; DNA -- Research -- Periodicals; 572.86072
• DOI: 10.1093/dnares/dsz003
• Languages: English
• ISSNs: 1340-2838

Abstract

Abstract: Urodele newts have unique biological properties, notably including prominent regeneration ability. The Iberian ribbed newt, Pleurodeles waltl, is a promising model amphibian distinguished by ease of breeding and efficient transgenic and genome editing methods. However, limited genetic information is available for P. waltl . We conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build and annotate gene models. We generated 1.2 billion Illumina reads from a wide variety of samples across 12 different tissues/organs, unfertilized egg, and embryos at eight different developmental stages. These reads were assembled into 1, 395, 387 contigs, from which 202, 788 non-redundant ORF models were constructed. The set is expected to cover a large fraction of P. waltl protein-coding genes, as confirmed by BUSCO analysis, where 98% of universal single-copy orthologs were identified. Ortholog analyses revealed the gene repertoire evolution of urodele amphibians. Using the gene set as a reference, gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Our transcriptome resource is expected to enhance future research employing this emerging model animal for regeneration research as well as for investigations in other areas including developmental biology, stem cell biology, and cancer research. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/ ).