Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed...

Area of Science:

• Genomics and Transcriptomics
• Animal Breeding and Genetics
• Molecular Biology

Background:

• Consumer and producer preference for thin-tailed sheep necessitates understanding tail fat deposition mechanisms.
• Post-transcriptional modifications, including alternative splicing (AS) and alternative polyadenylation (APA), are implicated in regulating sheep tail fat.
• Previous technological limitations hindered comprehensive analysis of these modifications and differentially expressed transcripts (DETs) in sheep tail fat.

Purpose of the Study:

• To investigate the transcriptomic complexity of sheep tail fat, focusing on post-transcriptional modification events.
• To identify differentially expressed transcripts (DETs) between thin-tailed and fat-tailed sheep.
• To uncover candidate genes and molecular mechanisms underlying tail fat deposition in sheep.

Main Methods:

• Pooled PacBio Isoform Sequencing (Iso-Seq) was employed to generate transcriptomic data from sheep tail fat.
• Comparison with reference genomes identified potential gene loci and novel transcripts.
• Iso-Seq data, combined with RNA-sequencing (RNA-Seq) data, was used to identify DETs, AS, APA events, and long non-coding RNAs (lncRNAs). Functional enrichment analyses (GO, KEGG, PPI) were performed.

Main Results:

• The study revealed significant transcriptomic complexity, identifying 9,001 novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs.
• Hundreds of DETs were identified between thin- and fat-tailed sheep, including 21 differentially expressed lncRNAs and novel transcripts associated with genes like DGAT2, ACSS2, ACLY, and SCD.
• Enrichment analyses indicated that most identified DETs are involved in pathways related to the extracellular matrix (ECM).

Conclusions:

• This research elucidates the intricate transcriptome of sheep tail fat, highlighting the roles of AS and APA in regulating fat deposition.
• Numerous candidate transcripts and novel genes influencing tail fat traits were identified, providing valuable targets for genetic improvement.
• The findings enhance the understanding of the molecular mechanisms governing tail fat deposition, crucial for breeding programs aimed at thin-tailed sheep.