# Improved transcriptome assembly and functional annotation of Pleurodeles waltl for regeneration research

## TL;DR

This paper improves the transcriptome and annotations of the Iberian ribbed newt to better study its regenerative abilities.

## Contribution

The study provides a more comprehensive and functionally annotated transcriptome using 67 libraries, including new data from key tissues.

## Key findings

- The new transcriptome assembly includes 58 published and 9 newly sequenced libraries, improving coverage of limb and heart tissues.
- Functional annotation was enhanced using Trinotate, adding ORFs, Pfam motifs, gene names, GO terms, and KEGG Orthology.
- Insights into limb regeneration and development were gained by examining key signaling pathways.

## Abstract

In this study, we present an updated transcriptome assembly for the Iberian ribbed newt, Pleurodeles waltl (P. waltl), a widely used model organism in regeneration research. The existing publicly available transcriptome for this species is limited by the inclusion of only three libraries from the limb and two from the heart, tissues of particular interest for regeneration studies. Additionally, the previous annotation was limited, reducing the utility of the dataset for further in-depth research. To provide a more complete transcriptome with a more comprehensive annotation, we utilized 58 previously published and 9 newly sequenced libraries, expanding the available transcriptomic data for key tissues, especially limb and heart tissues. Our assessment demonstrates that the new assembly offers a more comprehensive representation of reads and proteins compared to previous versions. Furthermore, we significantly improved the functional annotation by using the Trinotate pipeline, which includes the identification of complete ORFs, Pfam motifs, gene names, GO terms, and KEGG Orthology, facilitating more robust transcriptomic analyses. We also examined various stages of limb regeneration and development, gaining insights into the key signaling pathways involved. This work provides a valuable resource for researchers investigating the molecular mechanisms underlying P. waltl’s regenerative abilities, enabling more detailed gene expression studies and broader biological insights.