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首页> 外文期刊>Marine genomics >In silico whole-genome EST analysis reveals 2322 novel microsatellites for the silver-lipped pearl oyster, Pinctada maxima
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In silico whole-genome EST analysis reveals 2322 novel microsatellites for the silver-lipped pearl oyster, Pinctada maxima

机译：在计算机全基因组EST分析中，发现了2322个新的微卫星，用于银唇珍珠牡蛎Pinctada maxima

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摘要

Molecular stock improvement techniques such as marker assisted selection have great potential in accelerating selective breeding programmes for animal production industries. However, the discovery and application of trait/marker associations usually requires a large number of genome-wide polymorphic loci. Here, we present 2322 unique microsatellites for the silver-lipped pearl oyster, Pinctada maxima, a species of aquaculture importance throughout the Indo-Australian Archipelago for production of the highly valued South Sea pearl. More than 1.2 million Roche 454 expressed sequence tag (EST) reads were screened for microsatellite repeat motifs. A total of 12,604 sequences contained either a di, tri, tetra, penta or hexa microsatellite repeat motif (n≥6), with 6435 of these sequences having sufficient flanking regions for primer development. All identified microsatelliteswith designed primers were condensed into 2322 unique clusters (i.e., unique loci) of which 360 were shown to be polymorphic based on multiple sequence reads with different repeat motifs. Genotyping of five microsatellite loci demonstrated that in silico evaluation of polymorphism levels was a very useful method for identification of polymorphic loci, with the variation uncovered being a lower bound. Gene Ontology annotations of sequences containing microsatellites suggest that most are derived from a diverse array of unique genes. This EST derived microsatellite database will be a valuable resource for future studies in genetic map construction, diversity analysis, quantitative trait loci analysis, association mapping and marker assisted selection, not only for P. maxima, but also closely related species within the genus Pinctada.
机译：分子种群改良技术（例如标记辅助选择）在加速动物生产行业的选择性育种计划方面具有巨大潜力。然而，性状/标记关联的发现和应用通常需要大量的全基因组多态性基因座。在这里，我们为唇唇形牡蛎Pinctada maxima提供了2322个独特的微卫星，该牡蛎在整个印澳群岛中对水产养殖具有重要意义，可生产高价值的南洋珍珠。筛选了超过120万个Roche 454表达序列标签（EST）读数的微卫星重复基序。共有12,604个序列包含二，三，四，五或六微卫星重复基序（n≥6），其中6435个序列具有足够的侧翼区域用于引物开发。将所有鉴定的具有设计引物的微卫星浓缩为2322个独特的簇（即独特的基因座），其中基于具有不同重复基序的多个序列读数显示360个是多态的。对五个微卫星基因座的基因分型表明，对多态性水平进行计算机评估是鉴定多态性基因座的非常有用的方法，发现的变异为下限。包含微卫星的序列的基因本体论注释表明，大多数都源自一系列独特的基因。这个EST衍生的微卫星数据库将为将来在遗传图谱构建，多样性分析，数量性状基因座分析，关联图谱和标记辅助选择中的研究提供宝贵资源，不仅适用于P. maxima，而且适用于Pinctada属。

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