Development and application of a salmonid EST database and cDNA microarray: Data mining and interspecific hybridization characteristics
Development and application of a salmonid EST database and cDNA microarray: Data mining and interspecific hybridization characteristics
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DOI：
10.1101/gr.1687304
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发表时间：
2004-03-01
期刊：
影响因子：
7
通讯作者：
Koop, BF
中科院分区：
文献类型：
--
作者：
Rise, ML;von Schalburg, KR;Koop, BF
本研究共收集了23个大西洋鲑鱼(Salmo Salar)、6个虹鳟鱼(Oncorhynchus Mykis)、2个中华鲑鱼(Oncorhynchus Tshawytscha)、2个红鲑鱼(Oncorhynchus Nerka)、2个红鲑鱼(Oncorhynchus Nerka)、2个白鱼(Coregonus Clupeaformis)的80,388个EST。这些序列中的大多数是3个序列，可以区分由鲑鱼血统中最近的基因组复制引起的并列动物。序列组装发现28,710个不同的S.salar，8981个O.mykis，1085个O.tshawytscha，520个O.Nerka和1176个C Clupeaformis推定的转录本。我们根据分子功能对EST数据库中提交的部分进行了注释。文库中较高和较低分子量部分的文库显示包含不同的基因组，较高的基因发现率与较高相对分子质量的文库相关。幽门盲肠库群的注释表明，该器官可能在氧化还原控制中发挥作用，并作为一种屏障，阻止系统摄取外源物质。描述了一种包含7356个鲑鱼元素的微阵列，代表3557个不同的cDNA。对该基因芯片的跨物种杂交分析表明，该资源可用于涉及所有鲑类的研究。
We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3 sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. Salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C clupeaformis Putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for Studies involving all salmonids.