Digital expression profiling of novel diatom transcripts provides insight into their biological functions.
Digital expression profiling of novel diatom transcripts provides insight into their biological functions.
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DOI：
10.1186/gb-2010-11-8-r85
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发表时间：
2010
期刊：
影响因子：
12.3
通讯作者：
Bowler C
中科院分区：
文献类型：
--
作者：
Maheswari U;Jabbari K;Petit JL;Porcel BM;Allen AE;Cadoret JP;De Martino A;Heijde M;Kaas R;La Roche J;Lopez PJ;Martin-Jézéquel V;Meichenin A;Mock T;Schnitzler Parker M;Vardi A;Armbrust EV;Weissenbach J;Katinka M;Bowler C
硅藻是海洋中真核浮游植物的主要类群，负责全球约 20% 的光合作用。现在可以获得两个全基因组序列。尽管如此，我们对硅藻生物学的了解仍然有限，因为只有大约一半的基因可以根据基于同源性的方法归因于功能。因此，需要高通量工具将功能与硅藻特异性基因关联起来。我们对源自在 16 种不同条件下生长的三角褐指藻细胞的 130,000 个 EST 进行了系统分析。其中包括不同的氮源、不同浓度的二氧化碳、硅酸盐和铁，以及低温和低盐度等非生物胁迫。基于公正的统计方法，我们对具有相似表达谱的转录本进行了编目，并确定了对特定治疗反应差异表达的转录本。这些转录本的功能注释提供了对参与各种代谢和调节途径的基因的表达模式以及具有未知功能的新基因的作用的见解。特定的生长条件可能与增强的基因多样性、已知的基因产物功能和新转录本的过度表达有关。对另一种已测序硅藻（Thalassiosira fakenana）的数据进行比较分析，有助于识别在特定条件下受到专门调控的几种独特的硅藻基因，从而促进基因功能、基因组注释和物种多样性的分子基础的研究。数字基因表达数据库代表了一种新资源，用于识别参与主要生态相关过程的候选硅藻特异性基因。
Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.
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影响因子：
56.9
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Armbrust, EV;Berges, JA;Rokhsar, DS
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通讯作者：
Bowler, C