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United States Department of Agriculture

Agricultural Research Service

Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: Transcriptome assembly and digital gene expression atlas of the rainbow trout

Authors
item Paneru, Bam -
item Abdouni, Fatima -
item Thorgaard, Gary -
item Palti, Yniv
item Rexroad, Caird
item Yao, Jianbo -
item Salem, Mohamed -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 17, 2013
Publication Date: January 12, 2014
Citation: Paneru, B., Abdouni, F., Thorgaard, G.H., Palti, Y., Rexroad III, C.E., Yao, J., Salem, M. 2014. Transcriptome assembly and digital gene expression atlas of the rainbow trout. Plant and Animal Genome Conference. 249.

Technical Abstract: Background: Transcriptome analysis is a preferred method for gene discovery, marker development and gene expression profiling in non-model organisms. Previously, we sequenced a transcriptome reference using Sanger-based and 454-pyrosequencing, however, a transcriptome assembly is still incomplete and differential gene expression from various tissues was not studied. Result: Thirteen non-normalized cDNA libraries were sequenced from different tissues using Illumina sequencing. A total of ~1.167 billion paired-end reads were de novo assembled using Trinity assembler, which yielded 474,524 contigs (>500 bp), of them, 287,593 had significant homology to NCBI NR protein database. The longest contig of each contig cluster was selected as a reference which yielded 46,457 representative contigs. An EST-Scan of the representative contigs identified 45,291 transcripts with ORF, of them, 15,822 were full-length sequences. A digital gene expression atlas was generated by mapping original reads from each tissue to the new transcriptome reference. We identified 7,614 housekeeping and 4,830 tissues specific genes. Expression of about 17,000-33,000 genes seemed to account for both basic and specialized functions of each tissue, which corresponded to expression of 53%-70% of the total number of genes. Muscle and liver had the least complex transcriptome, with high percentage of their total mRNA contributed by a small number of genes, whereas brain and testis had the most complex transcriptome. The study also identified 4,752 genes with splice variants. Conclusion: This study provided the most comprehensive assembled and annotated transcriptomic suite of the rainbow trout that is available for functional, structural and comparative genomics research.

Last Modified: 4/19/2014
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