Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
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DOI：
10.1186/1471-2164-11-290
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发表时间：
2010-05-10
期刊：
影响因子：
4.4
通讯作者：
Butler, Geraldine
中科院分区：
文献类型：
--
作者：
Fitzpatrick, David A.;O'Gaora, Peadar;Butler, Geraldine
背景：念珠菌属是世界范围内机会性真菌感染的最常见原因。最近的测序工作提供了丰富的念珠菌基因组数据。我们已经开发了念珠菌基因顺序浏览器（CGOB），一个在线工具，有助于比较同线分析念珠菌物种。CGOB整合了所有可用的念珠菌进化枝基因组序列，包括两种白色念珠菌分离株（SC 5314和WO-1）和8种密切相关的菌种（都柏林念珠菌、热带念珠菌、近平滑念珠菌、长孢洛德酵母、汉逊德巴利酵母、树干毕赤酵母、季也蒙念珠菌和葡萄牙念珠菌）。酿酒酵母也包括作为一个参考genome.Results：CGOB分配的同源性手动策划的基础上序列相似性和同线性。CGOB总共包括65617个基因，排列成13625个同源列。我们还通过合并/去除每个基因组中的部分基因来产生改进的念珠菌基因集。对CGOB的查询显示，在所有念珠菌属物种中，大多数串联重复基因都处于强纯化选择下。我们确定了参与相同代谢途径的相邻基因簇（如生物素、半乳糖和N-乙酰葡糖胺的催化剂），并表明某些簇具有物种或谱系特异性。我们还确定了一个例子，内含子增益在C. albicands.Conclusions：我们的分析提供了一个重要的资源，现在可供念珠菌社区。CGOB可在http://cgob.ucd.ie上获得。
Background: Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of Candida species. CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Lodderomyces elongisporus, Debaryomyces hansenii, Pichia stipitis, Candida guilliermondii and Candida lusitaniae). Saccharomyces cerevisiae is also included as a reference genome.Results: CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C.albicans.Conclusions: Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie.