A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

Abstract

Background: Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish.

Results: 298,304 expressed sequence tags (ESTs) from Atlantic salmon (69% of the total), 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species.

Conclusion: An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94-96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is consistent with an ancestral salmonid genome duplication hypothesis. Genome resources, including a new 32 K microarray, provide valuable new tools to study salmonids.

Figure 1

Number of aligned contigs (y-axis) out of 81,398 total contigs is plotted against percent similarity of alignments (x- axis).

Figure 2

Screen shot of Atlantic salmon contig viewer. The top panel shows the alignment of 100/99 (first stage) clusters along with the number of individual EST reads in each. The second panel shows the 5 largest ORFs and reading frame, the BLASTX hits and reading frame, the Phred quality scores for each aligned position, and indicates whether TargetIdentifier has indicated that this clone is full-length and the predicted position of the START codon (green triangle). Selectable colored bars provide alignment links. The third panel gives specifics of the database hits and links to alignments and database entries.

Figure 3

Summary of 78 gene set consensus (70%) trees depicting the relationships among the major groups of Salmonidae. Each branch shows the number of consensus trees supporting the branch, the number of trees providing no information and the number of trees contradicting the branch. The diamond at the base of the Salmonidae cladogram indicates the position where the majority of gene duplications were identified. The individual gene trees that pertain to each branch position are indicated in Table 4.