A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology

Masatoshi Matsunami, Miyuki Suzuki, Yoshikazu Haramoto, Akimasa Fukui, Takeshi Inoue, Katsushi Yamaguchi, Ikuo Uchiyama, Kazuki Mori, Kosuke Tashiro, Yuzuru Ito, Takashi Takeuchi, Ken Ichi T. Suzuki, Kiyokazu Agata, Shuji Shigenobu, Toshinori Hayashi

Research output: Contribution to journalArticle

1 Citation (Scopus)

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/).

Original languageEnglish
Pages (from-to)217-229
Number of pages13
JournalDNA research : an international journal for rapid publication of reports on genes and genomes
Volume26
Issue number3
DOIs
Publication statusPublished - Jun 1 2019

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Pleurodeles
Salamandridae
Developmental Biology
Transcriptome
Regeneration
Gene Regulatory Networks
Amphibians
Genes
RNA Sequence Analysis
Gene Expression Profiling
Open Reading Frames
Breeding
Ovum
Cell Biology
Stem Cells
Embryonic Structures
Research
Neoplasms
Proteins

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology. / 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.

In: DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 26, No. 3, 01.06.2019, p. 217-229.

Research output: Contribution to journalArticle

Matsunami, M, Suzuki, M, Haramoto, Y, Fukui, A, Inoue, T, Yamaguchi, K, Uchiyama, I, Mori, K, Tashiro, K, Ito, Y, Takeuchi, T, Suzuki, KIT, Agata, K, Shigenobu, S & Hayashi, T 2019, 'A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology', DNA research : an international journal for rapid publication of reports on genes and genomes, vol. 26, no. 3, pp. 217-229. https://doi.org/10.1093/dnares/dsz003
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. / A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology. In: DNA research : an international journal for rapid publication of reports on genes and genomes. 2019 ; Vol. 26, No. 3. pp. 217-229.
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AU - Inoue, Takeshi

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