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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #347812

Research Project: Genetic and Genomic Approaches to Improve Swine Reproductive Efficiency

Location: Livestock Bio-Systems

Title: Additional annotation of the pig transcriptome using integrated Iso-seq and Illumina RNA-seq analysis

item BEIKI, HAMID - Iowa State University
item LIU, HAIBO - Iowa State University
item HUANG, JIANZHEN - Iowa State University
item MANCHANDA, NANCY - Iowa State University
item Nonneman, Danny - Dan
item Smith, Timothy - Tim
item TUGGLE, CHRIS - Iowa State University

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2017
Publication Date: 1/17/2018
Citation: Beiki, H., Liu, H., Huang, J., Manchanda, N., Nonneman, D.J., Smith, T.P.L., Tuggle, C.K. 2018. Additional annotation of the pig transcriptome using integrated Iso-seq and Illumina RNA-seq analysis. [abstract] In proceedings: Plant and Animal Genome Conference XXVI, San Diego, CA, 13-17 Jan 2018. Poster abstract P0439. Available:

Interpretive Summary:

Technical Abstract: Alternative splicing is a well-known phenomenon that dramatically increases eukaryotic transcriptome diversity. The extent of mRNA isoform diversity among porcine tissues was assessed using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq) and Illumina short read sequencing (RNA-seq) from a single individual White cross-bred pig. Isoseq data for nine tissues (brain, hypothalamus, liver, muscle, thymus, pituitary, small intestine, spleen and diaphragm) was error-corrected using RNA-seq data from the same RNA samples. Alignment of RNA-seq data to the current Ssc11.1 build (Ensembl release 90) for all 9 tissues revealed 401 tissue specific (TS) genes (50-fold higher FPKM level in one tissue compared with all others) and 8,309 housekeeping genes (FPKM=1 in all tissues). Interestingly, 262 TS genes had no Gene Ontology annotation. Integration of IsoSeq and RNAseq data in liver and brain tissues identified 17,086 expressed (RNAseq FPKM=1) novel isoforms (isoform that have at least one novel splice junction with an annotated transcript). Many expressed isoforms were detected within annotated intergenic (1,271) or intronic (801) regions. Many of these novel genes were validated using H3K36me3 (gene body mark) and H3K4me3 (promoter mark) ChIP-seq in liver. Analyses are ongoing for the other seven tissues, as well as tissue specific alternative splicing and long non-coding RNAs across all tissues. In summary, the results of this study can improve the incompletely annotated pig genome through the addition of alternative splicing complexity and identification of new features that are not included in the current pig genome annotation.