Abstract
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/
Highlights
Light is one of the major sources of energy and provides a signal for all living organisms from single cells to multicellular organisms
Evolution of cryptochromes Cryptochromes play a crucial role in the regulation of circadian rhythms
Cryptochromes are related to DNA photolyases, which play a role in DNA repair
Summary
Light is one of the major sources of energy and provides a signal for all living organisms from single cells to multicellular organisms. To identify putative genes that encode photolyases or cryptochromes, five subfamilies were defined based on previous research [9, 15], and protein domain profiling was performed (Table 1). To identify putative genes that encode cryptochromes, >7.5 million protein sequences from 1438 genomes in bacteria, archaea, oomycetes, fungi, plants and animals were screened.
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