1. Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology
- Author
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Beiki, Hamid, Murdoch, Brenda M, Park, Carissa A, Kern, Chandlar, Kontechy, Denise, Becker, Gabrielle, Rincon, Gonzalo, Jiang, Honglin, Zhou, Huaijun, Thorne, Jacob, Koltes, James E, Michal, Jennifer J, Davenport, Kimberly, Rijnkels, Monique, Ross, Pablo J, Hu, Rui, Corum, Sarah, McKay, Stephanie, Smith, Timothy PL, Liu, Wansheng, Ma, Wenzhi, Zhang, Xiaohui, Xu, Xiaoqing, Han, Xuelei, Jiang, Zhihua, Hu, Zhi-Liang, and Reecy, James M
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Generic health relevance ,Cattle ,Animals ,Gene Expression Profiling ,Genomics ,Sequence Analysis ,RNA ,Transcriptome ,Quantitative Trait Loci ,RNA ,Protein Isoforms ,Molecular Sequence Annotation ,functional genomics ,transcriptomics ,epi-genetics ,multi-omics integration ,trait-similarity network ,QTL - Abstract
BackgroundThe accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues.ResultsA total 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 isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated 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. Furthermore, we identified 3,744 genes that functioned as noncoding 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 quantitative trait loci data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network.ConclusionsThese validated results show significant improvement over current bovine genome annotations.
- Published
- 2024