Abstract
BackgroundSalmonids 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.Results298,304 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.ConclusionAn 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.
Highlights
Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture
Results and discussion cDNA libraries New, directionally cloned, mixed tissue, normalized cDNA libraries were constructed for Atlantic salmon (Salmo salar; European McConnell, and Canadian, Saint John River strains), chinook salmon (Oncorhynchus tschawytscha), sockeye salmon (Oncorhynchus nerka), brook trout (Salvelinus fontinalis), lake whitefish (Coregonus clupeaformis), grayling (Thymallus thymallus), and northern pike (Esox lucius)
There are a number of studies and good evidence, primarily from sequenced zebrafish and pufferfish genome sequences, for tetraploidization/rediploidization early in the ray-finned fish lineage (350–400 MYA) [13,14,15,16]. Several of these studies have suggested that the ancestral fish duplication, in addition to the two ancestral vertebrate genome duplications, are part of the reason why ray-finned fishes make up nearly half of all extant vertebrates species and exhibit tremendous biodiversity affecting their morphology, ecology, behavior and evolution
Summary
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. Extensive knowledge of trout and salmon is a result of their widespread use in scientific research, as an environmental sentinel species and as a food and sport fish. Perhaps more is known about the physiology, ecology, genetics, behavior and biology of salmonids than any other fish group [1]. This background provides a wealth of data from an economically important and phylogenetically distinct group of fish that can help guide, and benefit from, new genomic studies. Salmonids belong to a basal teleost Protacanthopterygii suborder (smelt, pike and salmon) group, which has been separated from other well studied euteleost lineages such as Ostariophysi (zebrafish, catfish, flathead minnow, etc.), and Acanthopterygii (cod, cichlids, fugu, sticklebacks, rockfish) for 217–290 MY [2,3,4,5]
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