Supporting data for "Enhanced Bovine Genome Annotation Through Integration of Transcriptomics and Epi-Genetics Datasets Facilitates Genomic Biology"

A total number of 160,820 unique transcripts (50% protein-coding) representing 34,882 unique genes (60% protein-coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio Iso-seq data, ONT-seq data, de novo assembled transcripts from RNA-seq data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as WTTS-seq, RAMPAGE, ChIP-seq, and ATAC-seq. A large proportion of identified transcripts (69%) were un-annotated, of which 86% were produced by annotated genes and 14% by un-annotated genes. A median of two 5 untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. <br>Furthermore, we identified 3,744 genes that functioned as non-coding genes in fetal tissues, but as protein coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available QTL data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. These validated results show significant improvement over current bovine genome annotations.