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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION AND CHARACTERIZATION OF GENES AFFECTING COOL AND COLD WATER AQUACULTURE PRODUCTION Title: Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approaches

Authors
item Salem, Mohamed -
item Rexroad, Caird
item Wang, Jiannan -
item Thorgaard, Gary -
item Yao, Jianbo -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 9, 2010
Publication Date: January 9, 2010
Citation: Salem, M., Rexroad III, C.E., Wang, J., Thorgaard, G.H., Yao, J. 2010. Characterization of the rainbow trout transcriptome using Sanger and 454-Pyrosequencing approaches. Plant and Animal Genome Conference, No. 101.

Technical Abstract: BACKGROUND: Rainbow trout is an important fish species for aquaculture and a model species for research investigations associated with carcinogenesis, comparative immunology, toxicology and the evolutionary biology. However, to date there is no genome reference sequence to facilitate the development of molecular technologies. Alternatively, transcriptome sequencing is a rapid and efficient means for gene discovery and genetic marker development. Although a large number of EST (258,973) sequences are publicly available for rainbow trout, the nature of its duplicated genome hinders assembly and complicates annotation. RESULTS: High-throughput deep sequencing of a rainbow trout double-haploid transcriptome using DNA 454-pyrosequencing technology yielded ~1.3 million reads with an average length of 344bp, a total of 447 million bases. De novo assembly of the sequences yielded 151,847 Tentative Consensus sequences (TCs)(Average length 662 nt) and 224,391 singletons. A combination assembly of both the 454-pyrosequencing ESTs and the pre-existing sequences resulted in 161,818 TCs (Average length 758 nt) and 261,071 singletons. Gene Ontology analysis of the combination assembly showed similarity to transcriptomes of other fish species with known genome sequences, suggesting a genome-wide representation of the rainbow trout transcriptome sequence. CONCLUSION: The 454 library significantly increased the suite of annotated EST sequences available for rainbow trout, thereby greatly improving assembly and annotation of the transcriptome. Furthermore, the 454 library is a new tool for functional genome research in rainbow trout, providing a wealth of sequence data;identifying putative paralogous sequence and/or allelic variation; and for digital gene expression and proteomic research in rainbow trout.

Last Modified: 10/25/2014
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