Pleurodeles Waltl Transcriptome assembly

<b>Files Description:</b><b>Trinity.min200.id.fsa.gz:</b> Pleurodeles Waltl transcriptome assembly fasta file.<b>Trinity_TRANSCRIPT2GENE_NAME.zip:</b> tx2gene table, use it with tximport R package to summarize transcripts counts into genes.<b>org.Pwaltl.eg.db.zip:</b> annotation package include the GO (Gene Ontology) and KO (KEGG Orthology) terms annotation. Use it with the summarized gene counts to perform enrichment analysis using the clusterProfiler R package. [to install in R use the command:<br>devtools::install_local("path/org.Pwaltl.eg.db.zip", repos = NULL, type="source") ]<b>trinotate_annotation_report.uniq.xls.gz:</b> Full annotation report from trinotate workflow (Swiss-Prot and TrEMBL, Pfam, GO terms, etc).<b>Trinity.cds.fsa.gz</b>, <b>Trinity.pep.fsa.gz:</b> ORF prediction and protein using transdecoder.<b>Limb_gene_counts_tximport.xlsx:</b> gene abundances and counts using tximport package with tx2gene table.<b>Limb_DEG.xlsx:</b> Differentially expressed genes in different limb stages when compared to 0dpa.<b>Limb_Enrichment_BP_KO.xlsx:</b> GO Biological Processes GSEA, and KO ortholog GSEA results in different limb stages when compared to 0dpa.<b>Commands.txt:</b> key commands used in the assembly process.<b>all_tissues_gene_counts_raw</b>: gene counts for all tissues analyzed.<b>all_tissues_gene_counts_vst</b>: VST counts for all tissues analyzed using DESeq2 package.<br><b>Abstract:</b>In this study, we present an updated transcriptome assembly for the Iberian ribbed newt, Pleurodeles waltl (<i>P. waltl</i>), 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 <i>P. waltl</i><i>'s</i> regenerative abilities, enabling more detailed gene expression studies and broader biological insights.

<b>文件说明：</b><br><b>Trinity.min200.id.fsa.gz：</b>伊比利亚肋突螈（Pleurodeles waltl）转录组组装FASTA格式压缩文件。<br><b>Trinity_TRANSCRIPT2GENE_NAME.zip：</b>tx2gene表格，需配合tximport R包使用，用于将转录本计数汇总为基因水平计数。<br><b>org.Pwaltl.eg.db.zip：</b>包含基因本体（Gene Ontology, GO）与KEGG同源基因（KEGG Orthology, KO）注释信息的注释包，可配合汇总后的基因计数数据，使用clusterProfiler R包开展富集分析。[R安装命令如下：<br>devtools::install_local("path/org.Pwaltl.eg.db.zip", repos = NULL, type="source") ]<br><b>trinotate_annotation_report.uniq.xls.gz：</b>来自Trinotate分析流程的完整注释报告（涵盖Swiss-Prot、TrEMBL、Pfam、GO条目等）。<br><b>Trinity.cds.fsa.gz</b>与<b>Trinity.pep.fsa.gz：</b>通过TransDecoder预测得到的开放阅读框（Open Reading Frame, ORF）序列及蛋白质序列文件。<br><b>Limb_gene_counts_tximport.xlsx：</b>配合tx2gene表格使用tximport包得到的基因丰度与计数数据。<br><b>Limb_DEG.xlsx：</b>与0dpa（截肢后0天）样本相比，不同肢体发育阶段的差异表达基因数据。<br><b>Limb_Enrichment_BP_KO.xlsx：</b>与0dpa样本相比，不同肢体发育阶段的GO生物过程（Biological Processes, BP）基因集富集分析（Gene Set Enrichment Analysis, GSEA）及KO同源基因GSEA结果。<br><b>Commands.txt：</b>转录组组装过程中使用的核心命令脚本。<br><b>all_tissues_gene_counts_raw：</b>所有分析组织的原始基因计数数据。<br><b>all_tissues_gene_counts_vst：</b>使用DESeq2 R包对所有分析组织进行方差稳定变换（Variance Stabilizing Transformation, VST）后的计数数据。<br><br><b>研究摘要：</b>本研究针对再生研究领域常用模式生物伊比利亚肋突螈（Pleurodeles waltl，<i>P. waltl</i>）发布了一套更新版转录组组装结果。该物种目前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，此前的注释信息较为匮乏，限制了该数据集在后续深入研究中的应用价值。为构建更完整的转录组并提供更全面的注释，本研究整合了58套已发表的测序文库与9套新测序文库，扩充了该物种重点组织（尤其是肢体与心脏组织）的转录组数据规模。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分析流程大幅优化了功能注释，涵盖完整开放阅读框（ORF）鉴定、Pfam结构域注释、基因名称标注、GO条目注释及KEGG同源基因注释，可支撑更严谨的转录组学分析。本研究同时分析了肢体再生与发育的多个阶段，解析了其中涉及的关键信号通路。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资源支撑，助力更精细的基因表达研究与更广泛的生物学认知拓展。