ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata
ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata
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DOI：
10.1186/1471-2164-8-269
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发表时间：
2007-08-08
期刊：
影响因子：
4.4
通讯作者：
Weigel, Detlef
中科院分区：
文献类型：
--
作者：
Dreyer, Christine;Hoffmann, Margarete;Weigel, Detlef
背景资料：孔雀鱼（Poecilia reticulata）是研究雄性孔雀鱼观赏性状遗传和变异以及对不同河流生境适应性的模式生物。然而，用于研究这一重要模式的基因组资源以前没有广泛提供。结果：与产生的分子标记的遗传作图的孔雀鱼，cDNA文库构建从胚胎和不同的成年器官，以产生表达序列标签（EST）的目的。根据BLASTX和BLASTX结果注释了约18，000个EST，并利用来自3'UTR的序列信息来产生PCR引物，用于对来自不同野生型菌株的基因组DNA进行重新测序。通过比较来自至少四种不同生态型的EST连锁基因组序列，鉴定出约1，700个多态性，代表约400个不同的基因。建立了两个互连的MySQL数据库，分别组织EST和标记。基于10个不同的核基因，重建了孔雀鱼的一个强大的系统发育。结论：我们的EST和标记数据库为孔雀鱼的遗传作图和系统发育研究提供了有用的工具。
Background: The guppy, Poecilia reticulata, is a well- known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available.Results: With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags ( ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST- linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes.Conclusion: Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.