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dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors.

Kim YM, Choi J, Lee HY, Lee GW, Lee YH, Choi D - Database (Oxford) (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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/

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The taxonomic distribution of the number of genes encoding the five cryptochrome subfamilies. The distribution of the 1306 identified cryptochromes is shown in the accumulated chart. The average number of genes in each of the five subfamilies (PC, plant-type cryptochrome; CD, CRY-DASH; PI, CPD photolyase class I; PII, CPD photolyase class II; AC, animal-type cryptochromes including 6–4 photolyase) is shown for each taxonomy.
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bau037-F2: The taxonomic distribution of the number of genes encoding the five cryptochrome subfamilies. The distribution of the 1306 identified cryptochromes is shown in the accumulated chart. The average number of genes in each of the five subfamilies (PC, plant-type cryptochrome; CD, CRY-DASH; PI, CPD photolyase class I; PII, CPD photolyase class II; AC, animal-type cryptochromes including 6–4 photolyase) is shown for each taxonomy.

Mentions: In total, 818 genomes have at least one of the putative genes from the photolyase/cryptochrome family, including genomes from 15 archaea, 561 bacteria, 150 fungi, 33 animals and 30 plants (Figure 2). Genes that belongs to CPD photolyase class I were the most frequently found; 621 genes were found in 590 genomes. Among these 590 genomes, 449 and 121 genomes belonged to bacteria and fungi, respectively, which indicates that the genomes of archaea, plants and animals rarely possess this type of blue-light regulator. The 74 plant-type cryptochromes were found only in the species belonging to the kingdom Plantae, with an exception in the subphylum Prasinophyceae. The number of genes encoding plant-type cryptochromes ranged from one to nine because of the varying number of alternatively spliced isoforms. In Oryza sativa, for example, six isoform products were captured among nine predicted plant-type cryptochromes. The genes encoding CRY-DASH proteins were distributed across a wide range of taxonomy, which is in accordance with previous research (20, 21). Unlike other classes, a low level of variance was observed in the number of CRY-DASH genes, which suggests that these genes do not have many alternative splicing isoforms. The genes encoding CPD photolyase class II were also found in a broad spectrum of taxa including bacteria, archaea, fungi, animals and plants but found in only 121 genomes. The genes encoding animal-type cryptochromes were also found in a broad spectrum of the taxa. In addition, high variance was detected in the phylum ‘Craniata’, ranging from 1 to 17, as shown in the high variance in plant-type cryptochromes (Figure 2).Figure 2.


dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors.

Kim YM, Choi J, Lee HY, Lee GW, Lee YH, Choi D - Database (Oxford) (2014)

The taxonomic distribution of the number of genes encoding the five cryptochrome subfamilies. The distribution of the 1306 identified cryptochromes is shown in the accumulated chart. The average number of genes in each of the five subfamilies (PC, plant-type cryptochrome; CD, CRY-DASH; PI, CPD photolyase class I; PII, CPD photolyase class II; AC, animal-type cryptochromes including 6–4 photolyase) is shown for each taxonomy.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016680&req=5

bau037-F2: The taxonomic distribution of the number of genes encoding the five cryptochrome subfamilies. The distribution of the 1306 identified cryptochromes is shown in the accumulated chart. The average number of genes in each of the five subfamilies (PC, plant-type cryptochrome; CD, CRY-DASH; PI, CPD photolyase class I; PII, CPD photolyase class II; AC, animal-type cryptochromes including 6–4 photolyase) is shown for each taxonomy.
Mentions: In total, 818 genomes have at least one of the putative genes from the photolyase/cryptochrome family, including genomes from 15 archaea, 561 bacteria, 150 fungi, 33 animals and 30 plants (Figure 2). Genes that belongs to CPD photolyase class I were the most frequently found; 621 genes were found in 590 genomes. Among these 590 genomes, 449 and 121 genomes belonged to bacteria and fungi, respectively, which indicates that the genomes of archaea, plants and animals rarely possess this type of blue-light regulator. The 74 plant-type cryptochromes were found only in the species belonging to the kingdom Plantae, with an exception in the subphylum Prasinophyceae. The number of genes encoding plant-type cryptochromes ranged from one to nine because of the varying number of alternatively spliced isoforms. In Oryza sativa, for example, six isoform products were captured among nine predicted plant-type cryptochromes. The genes encoding CRY-DASH proteins were distributed across a wide range of taxonomy, which is in accordance with previous research (20, 21). Unlike other classes, a low level of variance was observed in the number of CRY-DASH genes, which suggests that these genes do not have many alternative splicing isoforms. The genes encoding CPD photolyase class II were also found in a broad spectrum of taxa including bacteria, archaea, fungi, animals and plants but found in only 121 genomes. The genes encoding animal-type cryptochromes were also found in a broad spectrum of the taxa. In addition, high variance was detected in the phylum ‘Craniata’, ranging from 1 to 17, as shown in the high variance in plant-type cryptochromes (Figure 2).Figure 2.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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/

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