Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea and Center for Fungal Genetic Resources and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-742, Korea.
Database (Oxford). 2014 May 9;2014(0):bau037. doi: 10.1093/database/bau037. Print 2014.
Cryptochromes are flavoproteins that play a central role in the circadian oscillations of all living organisms except archaea. Cryptochromes are clustered into three subfamilies: plant-type cryptochromes, animal-type cryptochromes and cryptochrome-DASH proteins. These subfamilies are composed of photolyase/cryptochrome superfamily with 6-4 photolyase and cyclobutane pyrimidine dimer photolyase. Cryptochromes have conserved domain architectures with two distinct domains, an N-terminal photolyase-related domain and a C-terminal domain. Although the molecular function and domain architecture of cryptochromes are conserved, their molecular mechanisms differ between plants and animals. Thus, cryptochromes are one of the best candidates for comparative and evolutionary studies. Here, we have developed a Web-based platform for comparative and evolutionary studies of cryptochromes, dbCRY (http://www.dbcryptochrome.org/). A pipeline built upon the consensus domain profile was applied to 1438 genomes and identified 1309 genes. To support comparative and evolutionary genomics studies, the Web interface provides diverse functions such as (i) browsing by species, (ii) protein domain analysis, (iii) multiple sequence alignment, (iv) homology search and (v) extended analysis opportunities through the implementation of 'Favorite Browser' powered by the Comparative Fungal Genomics Platform 2.0 (CFGP 2.0; http://cfgp.snu.ac.kr/). dbCRY would serve as a standardized and systematic solution for cryptochrome genomics studies. Database URL: http://www.dbcryptochrome.org/
隐花色素是一种黄素蛋白，在所有除古菌以外的生物体的昼夜节律振荡中发挥核心作用。隐花色素分为三个亚家族：植物型隐花色素、动物型隐花色素和隐花色素-DASH 蛋白。这些亚家族由光解酶/隐花色素超家族组成，具有 6-4 光解酶和环丁烷嘧啶二聚体光解酶。隐花色素具有保守的结构域架构，由两个不同的结构域组成：N 端光解酶相关结构域和 C 端结构域。尽管隐花色素的分子功能和结构域架构是保守的，但它们在植物和动物中的分子机制是不同的。因此，隐花色素是比较和进化研究的最佳候选者之一。在这里，我们开发了一个基于网络的隐花色素比较和进化研究平台 dbCRY（http://www.dbcryptochrome.org/）。基于共识结构域图谱构建的流水线应用于 1438 个基因组，鉴定出 1309 个基因。为了支持比较和进化基因组学研究，该网络界面提供了多种功能，如（i）按物种浏览，（ii）蛋白质结构域分析，（iii）多序列比对，（iv）同源搜索，以及（v）通过实施由比较真菌基因组学平台 2.0（CFGP 2.0；http://cfgp.snu.ac.kr/）提供的“收藏夹浏览器”提供扩展分析机会。dbCRY 将成为隐花色素基因组学研究的标准化和系统解决方案。数据库网址：http://www.dbcryptochrome.org/
