VZV 2.0 annotation

This repository contains files related to our recent re-annotation of VZV strain Dumas described here - mBio .

All raw Illumina and Nanopore dRNA-Seq datasets associated with this study are available from the ENA under project accession PRJEB38829 .

Updates:

23.11.2021 - Fixed minor error with co-ordinates of VLT63 exons 24.08.2021 - Uploaded new version of GFF3 files and transcriptome file with minor fixes in genes 8 and 10, as well as in the VLT63 locus.

Description of files:

Annotation directory:

The major annotation files (GFF3 format) are found in the Annotation directory and comprise the following:

• VZV-Dumas-Forward-2.0.gff3 - GFF3 file denoting all VZV RNAs annotated along the top strand of VZV strain Dumas
• VZV-Dumas-Reverse-2.0.gff3 - GFF3 file denoting all VZV RNAs annotated along the bottom strand of VZV strain Dumas
• VZV_v2.0_complete.fasta - VZV 2.0 transcriptome file (multi-fasta) - contains all VZV transcripts present in the v2.0 annotation

Note: Users should ensure the header line in the genome fasta file matches the text used in column #1 of the GFF3 files prior to perform alignment and any downstream analyses

BED12 directory:

BED12 format files containing FLAIR-corrected read alignments are found in the BED12 folder and comprise the following:

• EMC1_ARPE19_12h_CHX_for_corr_all_corrected.bed

• EMC1_ARPE19_12h_CHX_rev_corr_all_corrected.bed

• EMC1_ARPE19_24h_PAA_for_corr_all_corrected.bed

• EMC1_ARPE19_24h_PAA_rev_corr_all_corrected.bed

• EMC1_ARPE19_24h_for_corr_all_corrected.bed

• EMC1_ARPE19_24h_rev_corr_all_corrected.bed

• EMC1_ARPE19_96h_for_corr_all_corrected.bed

• EMC1_ARPE19_96h_rev_corr_all_corrected.bed

• pOka_NEU_96h_for_corr_all_corrected.bed

• pOka_NEU_96h_rev_corr_all_corrected.bed

• pOka_ARPE19_96h_biorep1_for_corr_all_corrected.bed

• pOka_ARPE19_96h_biorep1_rev_corr_all_corrected.bed

• pOka_ARPE19_96h_biorep2_for_corr_all_corrected.bed

• pOka_ARPE19_96h_biorep2_rev_corr_all_corrected.bed

• VZV-Dumas.fasta - original VZV strain Dumas genome sequence in FASTA format (Genbank accession NC_001348.1). This version is compatible with BED12 files in IGV.

Note: these files were generated using nanopore dRNA-Seq datasets basecalled with Guppy v3.2.2

Note 2: BED12 filenames are constructured from VZV strain names (EMC1, pOka), infected cell type (ARPE-19 epithelial cells, hESC-derived neurons), infection period (12h, 24h, 96h), and treatment (cyclohexamide, phosphonoacetic acid) with the absence of CHX or PAA indicating no treatment was performed.