Endogenous giant viruses in polar microalgae

This project folder contains key information necessary for the manuscript "Extensive Array of Endogenous Giant Viral Elements in a Polar Alga Shows Dynamic Transcriptional Response to Abiotic Stress". 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:

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<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.

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.

Folder: Annotations: Functional annotation of the viral regions in 9 polar alga using four databases (Pfam, GVOG, NOG, VOG).
Folder: tnf_calculation_script: Python script, fasta file and viral region coordinate files to calculate and visualize TNF profiles of viral and non-viral regions of Chlamydomonas ICE-L genome.