UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
BMC Genomics. 2010 May 10;11:290. doi: 10.1186/1471-2164-11-290.
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.
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.
Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie.
念珠菌属是全球最常见的机会性真菌感染的病原体。最近的测序工作为念珠菌属的基因组数据提供了丰富的资源。我们开发了念珠菌基因顺序浏览器（CGOB），这是一种在线工具，可辅助念珠菌属物种的比较同线性分析。CGOB 整合了所有可用的念珠菌属谱系基因组序列，包括两个白色念珠菌分离株（SC5314 和 WO-1）和 8 个密切相关的种（都柏林念珠菌、热带念珠菌、近平滑念珠菌、 elongisporus 毕赤酵母、汉逊德巴利酵母、毕赤酵母、假丝酵母和葡萄牙念珠菌）。酿酒酵母也被包括作为参考基因组。
基于序列相似性和同线性，CGOB 的同源性分配经过人工整理。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，生成了改进的念珠菌基因集。CGOB 的查询结果表明，大多数串联重复基因在所有念珠菌属物种中都受到强烈的纯化选择。我们鉴定了参与同一代谢途径（如生物素、半乳糖和 N-乙酰葡萄糖胺的分解代谢）的相邻基因簇，并表明一些基因簇是物种或谱系特异性的。我们还鉴定了白色念珠菌中一个内含子获得的例子。
我们的分析为念珠菌社区提供了一个重要的资源。CGOB 可在 http://cgob.ucd.ie 上获取。
Zotero 插件
