Comparative genome analysis and gene finding in Candida species using CGOB.
Comparative genome analysis and gene finding in Candida species using CGOB.
复制标题
DOI：
10.1093/molbev/mst042
复制
发表时间：
2013-06
影响因子：
10.7
通讯作者：
Butler G
中科院分区：
文献类型：
--
作者：
Maguire SL;ÓhÉigeartaigh SS;Byrne KP;Schröder MS;O'Gaora P;Wolfe KH;Butler G
念珠菌基因顺序浏览器 (CGOB) 被开发为一种工具，用于可视化和分析多个念珠菌物种的同线性关系，并为进化分析提供一组准确的、手动策划的直系同源念珠菌基因。在这里，我们描述了 CGOB 的主要改进。数据库的底层结构发生了显着变化。基因组特征现在直接基于基因组注释而不是蛋白质序列，这允许包括非蛋白质特征，例如白色念珠菌的着丝粒位置和所有物种的 tRNA 基因。该数据集已扩展到 13 个物种，包括病原体基因组（白色念珠菌、近平滑念珠菌、热带念珠菌和直丝念珠菌），以及具有重要生物技术应用的木糖降解物种的基因组（细念珠菌、树干树干酵母和 Spathaspora passalidarum）。已纳入 C. parapsilosis、C. dubliniensis 和 Debaryomyces hansenii 的更新注释。我们在 13 个基因组中发现了 1,500 多个以前未注释的基因，大小从 29 到 3,850 个氨基酸不等。还发现了保守性差且快速进化的基因。对木糖降解者交配型基因座的重新分析表明，C. tenuis 是异宗合的，而 Spa. passalidarum 和 Stipitis 是同宗的。除了托管浏览器之外，CGOB 网站 (http://cgob.ucd.ie) 还可以直接访问所有底层基因组注释、序列和精选的直系同源数据。
The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The underlying structure of the database has been changed significantly. Genomic features are now based directly on genome annotations rather than on protein sequences, which allows non-protein features such as centromere locations in Candida albicans and tRNA genes in all species to be included. The data set has been expanded to 13 species, including genomes of pathogens (C. albicans, C. parapsilosis, C. tropicalis, and C. orthopsilosis), and those of xylose-degrading species with important biotechnological applications (C. tenuis, Scheffersomyces stipitis, and Spathaspora passalidarum). Updated annotations of C. parapsilosis, C. dubliniensis, and Debaryomyces hansenii have been incorporated. We discovered more than 1,500 previously unannotated genes among the 13 genomes, ranging in size from 29 to 3,850 amino acids. Poorly conserved and rapidly evolving genes were also identified. Re-analysis of the mating type loci of the xylose degraders suggests that C. tenuis is heterothallic, whereas both Spa. passalidarum and S. stipitis are homothallic. As well as hosting the browser, the CGOB website (http://cgob.ucd.ie) gives direct access to all the underlying genome annotations, sequences, and curated orthology data.
登录
查看更多内容
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
64.8
作者：
Dujon, B;Sherman, D;Souciet, JL
通讯作者：
Souciet, JL
影响因子：
4.4
作者：
Fitzpatrick, David A.;O'Gaora, Peadar;Butler, Geraldine
通讯作者：
Butler, Geraldine
影响因子：
7
作者：
Jackson, Andrew P.;Gamble, John A.;Berriman, Matthew
通讯作者：
Berriman, Matthew
影响因子：
3.4
作者：
Fitzpatrick, David A.;Logue, Mary E.;Butler, Geraldine
通讯作者：
Butler, Geraldine