Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): Mining and characterization of new genomic and molecular markers
Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): Mining and characterization of new genomic and molecular markers
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DOI：
10.1016/j.margen.2011.05.002
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发表时间：
2011-09-01
期刊：
影响因子：
1.9
通讯作者：
Tanguy, Arnaud
中科院分区：
文献类型：
--
作者：
Cardenas, Leyla;Sanchez, Roland;Tanguy, Arnaud
海洋腹足动物Concholepas concholepas在当地被称为“loco”，是智利底栖渔业的主要目标物种。遗传和基因组工具是必要的，以研究该物种的基因组，以了解其发展，增长的分子基础，和其他关键性状，以改善管理策略，并确定当地的适应，以防止生物多样性的丧失。在这里，我们使用焦磷酸测序技术从loco的成人标本中生成第一个转录组数据库。修剪后，获得总共140，756个表达序列标签序列。聚类和组装分析确定了19，219个重叠群和105，435个单一序列。BlastN分析表明，与公共数据库中不同腹足类物种的表达序列标签具有显著的一致性。同样，BlastX结果显示，在总共124，654个基因中，只有895个具有显著的命中，可能代表海洋腹足类的新基因。从这个数据库中，简单的序列重复基序也被确定，共38个引物对的设计和测试，以评估其潜在的信息标记，并调查其跨物种扩增在不同的相关腹足类物种。该数据集代表了第一个公开的454个数据的海洋腹足动物特有的东南太平洋沿岸，提供了一个宝贵的转录组资源，为未来的努力，基因发现和功能标记的开发在其他海洋腹足动物。(C)2011爱思唯尔有限公司版权所有。
The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods. (C) 2011 Elsevier B.V. All rights reserved.