Comparison of transcriptome assembly statistics.

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.本研究针对伊比利亚肋突螈（Iberian ribbed newt，*Pleurodeles waltl*，简称P. waltl）提供了一套更新的转录组组装结果，该物种是再生研究领域广泛使用的模式生物。目前该物种公开可用的转录组数据存在局限：仅包含3个肢体组织文库与2个心脏组织文库，而这两类组织正是再生研究的重点关注对象。此外，既往的转录组注释不够完善，降低了该数据集用于后续深入研究的实用价值。为构建更完整的转录组并提供更为全面的注释，本研究整合了58个已发表的转录组文库与9个新测序的文库，扩充了重点组织（尤其是肢体与心脏组织）的转录组数据储备。评估结果显示，相较于既往版本，本次更新的组装结果可更全面地覆盖测序读段与蛋白质序列。此外，本研究通过Trinotate注释流程显著优化了功能注释内容，涵盖完整开放阅读框（Open Reading Frame, ORF）鉴定、Pfam结构域注释、基因名称标注、基因本体（Gene Ontology, GO）术语注释以及KEGG同源基因（KEGG Orthology）注释，可为更可靠的转录组分析提供支撑。本研究同时分析了肢体再生与发育的多个关键阶段，进而对其中涉及的核心信号通路获得了更为深入的认知。本研究成果可为探索伊比利亚肋突螈再生能力背后的分子机制的研究人员提供宝贵的科研资源，助力更精细的基因表达研究与更广泛的生物学研究发现。