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.