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Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood
Published on: November 28, 2018
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A high-quality annotated transcriptome of swine peripheral blood
Haibo Liu1, Timothy P L Smith2, Dan J Nonneman2
1Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, 2258 Kildee Hall, Ames, IA, 50011, USA.
BMC Genomics
|June 26, 2017
Summary
Researchers developed a comprehensive pig blood transcriptome, improving gene expression analysis for biomedical research. This new resource enhances pig genome annotation and supports high-throughput transcriptomic assays.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- High-throughput gene expression profiling of peripheral blood is crucial in biomedicine and animal research.
- Accurate interpretation requires well-characterized reference genomes and transcriptomes.
- The pig reference genome and blood transcriptome are currently insufficient for robust profiling.
Purpose of the Study:
- To assemble and annotate a comprehensive porcine blood transcriptome.
- To integrate de novo and genome-guided assembly methods.
- To provide a foundational resource for pig biomedical research.
Main Methods:
- Assembled porcine whole peripheral blood transcriptome using Trinity and Cufflinks software.
- Integrated ~6 billion RNA-seq reads from 146 libraries.
- Validated transcripts using PacBio IsoSeq, NCBI RefSeq, Ensembl annotations, and CAGE data.
Main Results:
- Created an integrated transcriptome of 132,928 putative transcripts (PTs).
- Annotated PTs with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
- Identified numerous transcripts with improved or novel annotations compared to existing databases.
Conclusions:
- Developed and validated a comprehensive, well-annotated pig blood transcriptome.
- Significantly improved upon Ensembl Sscrofa10.2 and NCBI RefSeq mRNA annotations.
- Established a foundation for high-throughput transcriptomic assays and pig genome annotation.
