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><b>Trinity.min200.id.fsa.gz：</b>伊比利亚肋突螈（*Pleurodeles waltl*）转录组组装FASTA压缩文件。<b>Trinity_TRANSCRIPT2GENE_NAME.zip：</b>tx2gene表，可配合tximport R包将转录本计数汇总为基因计数。<b>org.Pwaltl.eg.db.zip：</b>包含基因本体（Gene Ontology，GO）与KEGG正交（KEGG Orthology，KO）注释的注释包，可配合汇总后的基因计数，通过clusterProfiler R包进行富集分析。R语言安装命令为：devtools::install_local("path/org.Pwaltl.eg.db.zip", repos = NULL, type="source")<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术语等）。<b>Trinity.cds.fsa.gz</b>、<b>Trinity.pep.fsa.gz：</b>经TransDecoder预测得到的开放阅读框（Open Reading Frame，ORF）编码序列与蛋白质序列FASTA压缩文件。<b>Limb_gene_counts_tximport.xlsx：</b>使用tximport包结合tx2gene表得到的基因丰度与计数数据。<b>Limb_DEG.xlsx：</b>以0dpa为对照的不同肢体阶段差异表达基因数据。<b>Limb_Enrichment_BP_KO.xlsx：</b>以0dpa为对照的不同肢体阶段GO生物过程（Biological Process，BP）基因集富集分析（Gene Set Enrichment Analysis，GSEA）与KO同源基因集富集分析结果。<b>Commands.txt：</b>组装过程中使用的关键命令。<b>all_tissues_gene_counts_raw：</b>所有分析组织的原始基因计数数据。<b>all_tissues_gene_counts_vst：</b>使用DESeq2包得到的所有分析组织的方差稳定转换（Variance Stabilizing Transformation，VST）计数数据。<br><b>摘要：</b>本研究针对伊比利亚肋突螈（*Pleurodeles waltl*，*P. waltl*）发布了更新版转录组组装结果。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仅包含3个肢体组织文库与2个心脏组织文库，存在样本局限性，且既往注释不够完善，限制了该数据集在后续深入研究中的应用价值。为提供更完整的转录组数据与更全面的注释，本研究整合了58个已发表文库与9个新测序文库，扩充了包括肢体与心脏在内的关键组织的转录组数据量。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流程完善了功能注释，包括完整开放阅读框鉴定、Pfam结构域注释、基因名称标注、GO术语与KO注释，为更稳健的转录组分析提供了支撑。本研究还分析了肢体再生与发育的多个阶段，解析了其中关键信号通路的作用机制。本工作为探索*P. waltl*再生能力背后的分子机制提供了宝贵的研究资源，可支持更精细的基因表达研究与更广泛的生物学洞察。