一项鲑科鱼类EST基因组研究：基因、重复、系统发育与微阵列
A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
作者信息
Koop Ben F, von Schalburg Kristian R, Leong Jong, Walker Neil, Lieph Ryan, Cooper Glenn A, Robb Adrienne, Beetz-Sargent Marianne, Holt Robert A, Moore Richard, Brahmbhatt Sonal, Rosner Jamie, Rexroad Caird E, McGowan Colin R, Davidson William S
机构信息
Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W3N5, Canada.
出版信息
BMC Genomics. 2008 Nov 17;9:545. doi: 10.1186/1471-2164-9-545.
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.
背景
鲑科鱼类因其相对近期的基因组复制，以及在野生渔业和水产养殖中的广泛应用而备受关注。一份全面的基因列表以及对一些不同物种基因的比较，为这一研究最为广泛的鱼类群体之一提供了有价值的基因组信息。
结果
本研究获得了来自大西洋鲑的298,304个表达序列标签（EST）（占总数的69%）、奇努克鲑的11,664个、红大马哈鱼的10,813个、溪红点鲑的10,051个、河鲈的10,975个、湖白鲑的8,630个以及北美狗鱼的3,624个EST，并已存入公共数据库。构建了重叠群并鉴定出了推定的全长大西洋鲑克隆。现有一个包含EST、组装序列、共有序列、开放阅读框、基因预测和推定注释的数据库。大西洋鲑EST与虹鳟、奇努克鲑、红大马哈鱼、溪红点鲑、河鲈、湖白鲑、北美狗鱼和虹银汉鱼EST的总体相似度分别为93.4%、94.2%、94.6%、94.4%、92.5%、91.7%、89.6%和86.2%。对78个转录本组的分析表明，鲑属在鲑亚科内是大麻哈鱼属和红点鲑属的姐妹群，茴鱼亚科在鲑科内是鲑亚科和白鲑亚科的姐妹群。广泛的基因复制与鲑科鱼类共同祖先中的基因组复制一致。利用所有可用的EST数据，创建了一个新的包含32,000个特征的扩展鲑科鱼类cDNA微阵列。与该cDNA微阵列的跨物种杂交表明，这一资源将对所有68种鲑科鱼类的研究有用。
结论
对鲑科鱼类RNA推定转录本的广泛收集和分析表明，太平洋鲑、大西洋鲑和红点鲑的相似度为94 - 96%，而亲缘关系较远的白鲑、河鲈、狗鱼和银汉鱼与鲑的相似度分别为93%、92%、89%和86%。鲑科鱼类转录组揭示了一个复杂的基因复制历史，这与祖先鲑科鱼类基因组复制假说一致。包括新的32K微阵列在内的基因组资源为研究鲑科鱼类提供了有价值的新工具。
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