RT Journal Article
SR Electronic
T1 Functional genomics of cattle through integration of multi-omics data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.10.05.510963
DO 10.1101/2022.10.05.510963
A1 Hamid Beiki
A1 Brenda M. Murdoch
A1 Carissa A. Park
A1 Chandlar Kern
A1 Denise Kontechy
A1 Gabrielle Becker
A1 Gonzalo Rincon
A1 Honglin Jiang
A1 Huaijun Zhou
A1 Jacob Thorne
A1 James E. Koltes
A1 Jennifer J. Michal
A1 Kimberly Davenport
A1 Monique Rijnkels
A1 Pablo J. Ross
A1 Rui Hu
A1 Sarah Corum
A1 Stephanie McKay
A1 Timothy P.L. Smith
A1 Wansheng Liu
A1 Wenzhi Ma
A1 Xiaohui Zhang
A1 Xiaoqing Xu
A1 Xuelei Han
A1 Zhihua Jiang
A1 Zhi-Liang Hu
A1 James M. Reecy
YR 2022
UL http://biorxiv.org/content/early/2022/10/06/2022.10.05.510963.abstract
AB Functional annotation of the bovine genome was performed by characterizing the spectrum of RNA transcription using a multi-omics approach, combining long- and short-read transcript sequencing and orthogonal data to identify promoters and enhancers and to determine boundaries of open chromatin. A total number of 171,985 unique transcripts (50% protein-coding) representing 35,150 unique genes (64% protein-coding) were identified across tissues. Among them, 159,033 transcripts (92% of the total) were structurally validated by independent datasets such as PacBio Iso-seq, ONT-seq, de novo assembled transcripts from RNA-seq, or Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive independent data from different technologies such as WTTS-seq, RAMPAGE, ChIP-seq, and ATAC-seq. A large proportion of identified transcripts (69%) were novel, of which 87% were produced by known genes and 13% by novel genes. A median of two 5’ untranslated regions was detected per gene, an increase from Ensembl and NCBI annotations (single). 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 non-coding genes in fetal tissues, but as protein coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 known 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.Competing Interest StatementThe authors have declared no competing interest.