GEVE region annotations

This project folder contains key information necessary for the manuscript "<b>Extensive Array of Endogenous Giant Viral Elements in a Polar Alga Shows Dynamic Transcriptional Response to Abiotic Stress</b>". The dataset provided includes functional annotations, raw data on gene expression and phylogenetic trees.What follows is a brief description of the content of each folder/file:<br><br>Folder: Confirmed_viral_region_faa - This folder contains predicted proteins (fasta protein) from the confirmed viral regions in each of the 9 polar algal genomes.Folder: Confirmed_VR_fna - This folder contains the complete viral regions (fasta nucleotide) from each of the 9 polar algal genomes. Folder: Differential_expression_analysis - This folder contains data on differential expression of viral region genes in Chlamydomonas sp. ICE-L in response to different stressors. File: ICEL_vr_readcounts.csv: Raw read counts for individual genes per treatment obtained from coverM mapping of the trimmed read libraries. File: rpkm_reads_alltreatments.csv: Reads per kilobase per million (RPKM) values denoting expression levels of the viral region genes. File: Significantly_Differentially_ExpressedGenes_per_treatment.xlsx: Spreadsheet with stats on genes with significantly different expression (q&lt;0.05) in response to different stress treatments. Log2foldchange and adjusted p values (padj) are provided along with other statistics. File: TransposableElement_Heatmap_DifferentialExpression.csv: A subset of genes from the DE analysis result representing expression of transposable elements across different treatments. Folder: MarkerGene_hits: Best hits of Viral region genes to different Nucleocytoviricota marker genes.<br>Folder: Trees: Phylogenetic trees and associated alignments for the phylogenetic reconstruction performed in this study. Trees of 9 Nucleocytoviricota hallmark genes and Ice-binding proteins (IBPs) are provided.<br>Folder: Annotations: Functional annotation of the viral regions in 9 polar alga using four databases (Pfam, GVOG, NOG, VOG).<br>