Leite Ricardo B, Milan Massimo, Coppe Alessandro, Bortoluzzi Stefania, dos Anjos António, Reinhardt Richard, Saavedra Carlos, Patarnello Tomaso, Cancela M Leonor, Bargelloni Luca
CCMAR- Center of Marine Sciences/University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
BMC Genomics. 2013 Oct 29;14:741. doi: 10.1186/1471-2164-14-741.
The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis.
A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed.
This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.
交错沟纹蛤（Ruditapes decussatus）是欧洲本土蛤类，从美食和经济角度来看是最受青睐的。由于多种因素，如帕金虫病、栖息地入侵以及外来入侵物种菲律宾蛤仔（Ruditapes philippinarum）的竞争，其产量正在下降。在对交错沟纹蛤转录组进行测序后，我们设计了一种寡核苷酸微阵列，能够为了解蛤类对帕金虫病的分子反应提供一些线索。
构建了一个由41119个独特转录本组成的数据库，其中12479个（30.3%）通过相似性进行了注释。然后设计了一个寡核苷酸DNA微阵列平台，并应用于分析受奥尔森帕金虫（Perkinsus olseni）严重感染的交错沟纹蛤中的基因表达。通过基因集富集分析对这两种条件下差异表达基因进行功能注释。正如预期的那样，微阵列揭示了与应激/感染因子相关的基因，如水解酶、蛋白酶等。还分析了先天免疫系统的广泛作用，并综述了寄生虫病对凝集素等重要分子表达的影响。
本研究首次尝试对交错沟纹蛤转录组进行表征，交错沟纹蛤是欧洲水产养殖的重要海洋资源。转录组测序及后续注释将增加该物种可用的工具和资源，引入了高通量实验如微阵列分析的可能性。在这个特定案例中，微阵列方法用于揭示交错沟纹蛤和帕金虫这两个非模式物种之间宿主 - 寄生虫相互作用的一些重要方面，突出了一些与这种相互作用相关的基因。获得了大量信息，以确定在受帕金虫感染与未感染的鳃中差异表达基因中显著富集的生物学过程。还报道了交错沟纹蛤转录组中与免疫系统相关基因的概述。
