Pérez Franklin, Ortiz Juan, Zhinaula Mariuxi, Gonzabay Cesar, Calderón Jorge, Volckaert Filip A M J
Fundación CENAIM-ESPOL, Km. 30.5 Viá Perimetral, Campus Politécnico, Guayaquil, Ecuador.
Mar Biotechnol (NY). 2005 Sep-Oct;7(5):554-69. doi: 10.1007/s10126-004-5099-1. Epub 2005 Jul 14.
We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa.
我们报告了对公开可得的凡纳滨对虾表达序列标签（ESTs）进行数据挖掘以生成简单序列重复（SSRs）标记，以及这些标记在相关对虾物种间的可转移性。在3.8%的评估ESTs中发现了重复基序，频率为每7.8 kb序列数据中有一个重复。总共设计了206对引物，其中112个位点在凡纳滨对虾中扩增成功率最高。很高比例（69%）的EST-SSRs在凡纳滨对虾属内可转移。在一个小的凡纳滨对虾测试群体中，超过一半的扩增产物具有多态性。在一个更大的测试群体中对这些引物进行评估表明，72%的标记符合哈迪-温伯格平衡，这表明它们在群体遗传分析中的实用性。此外，对一组26个EST-SSRs进行了孟德尔分离评估。通过单链构象多态性分析，发现相当比例（46%）的单态标记具有多态性。由于公共数据库中有大量的ESTs，类似于本文所述的数据挖掘方法可能会在许多动物类群中产生大量的SSR标记。
