The transcriptional and translational landscape of equine torovirus

Hazel Stewart; Katherine Brown; Adam M. Dinan; Nerea Irigoyen; Eric J. Snijder; Andrew E. Firth

Differential transcript abundance analysis was performed using the standard DESeq2 671 (64) pipeline described in the vignette. Genes to which <10 reads mapped were 672 discarded and shrinkage of log 2 fold changes for lowly expressed genes was 673 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/296996 doi: bioRxiv preprint performed using the lfcshrink method of DESeq2. All recommended quality control 674 plots were inspected, and no major biases were identified in the data. False 675 discovery rate (FDR) values were calculated using the R fdrtool package (65). Genes 676 with a log 2 fold change >1 and an FDR less than 0.1 were considered to be 677 differentially expressed. Gene ontology (GO) term enrichment analysis (66) was 678 performed against a background of all horse protein-coding genes in the Ensembl gtf 679 using a Fisher Exact Test and corrected for multiple testing with a Bonferroni 680 correction. GO annotations for horse genes were downloaded from BiomaRt 681 (Ensembl release 90) (67). Differential translational efficiency analysis was carried 682 out using the CDS counts table, normalised using the DESeq2 "sizeFactors" 683 technique. Similar to the differential transcription analysis, genes to which <10 reads 684 mapped were discarded. Again all recommended quality control plots for DESeq2 685 were inspected and no major biases were identified in the data. Differential 686 translation efficiency analysis was performed using Xtail (68), following the standard 687 pipeline described in the vignette. P-values were adjusted automatically within Xtail 688 using the Benjamini-Hochberg method. Genes with a log 2 fold change >1 and an 689 adjusted p-value less than 0.1 were considered to be differentially translated. GO 690 enrichment analysis was performed as described for the differential transcript 691 abundance analysis. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/296996 doi: bioRxiv preprint tree topology, dN/dS was calculated with codeml. The standard deviation for the 705 codeml dN/dS value was estimated via a bootstrapping procedure, in which codon 706 columns of the alignment were randomly resampled (with replacement); 100 707 randomized alignments were generated, and their dN/dS values calculated with 708