A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
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DOI：
10.1186/1471-2164-9-545
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发表时间：
2008-11-17
期刊：
影响因子：
4.4
通讯作者：
Davidson, William S.
中科院分区：
文献类型：
--
作者：
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., III;McGowan, Colin R.;Davidson, William S.
鲑鱼之所以引起人们的兴趣，是因为它们相对较新的基因组复制，以及它们在野生渔业和水产养殖中的广泛使用。一份全面的基因清单和一些不同物种的基因比较，为研究最广泛的鱼类之一提供了宝贵的基因组信息。本研究共获得298,304条表达序列标签(EST)，分别来自大西洋鲑鱼(占总数的69%)、中华鲑鱼(11,664条)、红鱼(10,813条)、鲑鱼(10,051条)、灰鱼(10,975条)、白鱼(8,630条)和北方狗鱼EST(3,624条)。构建了重叠群，并鉴定了假定的全长大西洋鲑鱼克隆。一个包含EST、组装、共识序列、开放阅读框架、基因预测和推定注释的数据库可用。大西洋鲑鱼EST序列与虹鲑鱼、斑点鲑鱼、红眼鱼、斑点鲑鱼、灰鲑鱼、湖白鱼、北梭鱼和彩虹鱼EST序列的相似性分别为93.4%、94.2%、94.6%、94.4%、92.5%、91.7%、89.6%和86.2%。对78个转录组的分析表明，Salmo在Salmoninae中是Oncorhynchus和Salvelinus的姊妹群，而Thymallinae在Salmonidae中是Salmoninae和Coregoninae的姊妹群。广泛的基因复制与鲑科动物共同祖先的基因组复制是一致的。利用所有可用的EST数据，创建了一个包含32,000个特征的新的扩展鲑鱼cDNA微阵列。与该基因芯片的跨物种杂交表明，该资源将对所有68种鲑鱼的研究有用。大量收集和分析鲑类RNA的推测转录本表明，太平洋鲑鱼、大西洋鲑鱼和Charr的相似性为94%-96%，而较远的白鱼、灰鲑鱼、梭子鱼和气味鲑鱼的相似性为93、92、和86%。鲑鱼转录组揭示了基因复制的复杂历史，这与祖先鲑鱼基因组复制假说是一致的。基因组资源，包括一个新的32K微阵列，为研究鲑鱼提供了有价值的新工具。
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. 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. 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.
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影响因子：
3.7
作者：
HAMPEL, FR
通讯作者：
HAMPEL, FR
影响因子：
3.1
作者：
Danzmann, RG;Cairney, M;Woram, RA
通讯作者：
Woram, RA
影响因子：
11.4
作者：
Hoegg, S;Meyer, A
通讯作者：
Meyer, A
影响因子：
4.4
作者：
Lukacs MF;Harstad H;Grimholt U;Beetz-Sargent M;Cooper GA;Reid L;Bakke HG;Phillips RB;Miller KM;Davidson WS;Koop BF
通讯作者：
Koop BF
影响因子：
3.1
作者：
McKay, SJ;Trautner, J;Devlin, RH
通讯作者：
Devlin, RH