4.8 Article

CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria

Journal

NUCLEIC ACIDS RESEARCH
Volume 50, Issue D1, Pages D758-D764

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab891

Keywords

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Funding

  1. National Natural Science Foundation of China [31871303]
  2. Open Funding Project of the State Key Laboratory of Biocatalysis and Enzyme Engineering [SKLBEE2019015]
  3. Key Laboratory of Biofuel, Chinese Academy of Sciences [CASKLB201802]
  4. State Key Laboratory of Freshwater Ecology and Biotechnology [2018FB09]

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CyanoOmicsDB is a database aiming to provide comprehensive functional information for cyanobacterial genes, with over 8 million entries from 928 genomes. It integrates transcriptional and translational profiles, gene function predictions, protein sequences, homologs, and more, offering researchers in this field a convenient way to access functional information on cyanobacterial genes. Compared to other existing databases, CyanoOmicsDB stands out for its extensive datasets and comprehensive functional information.
With their photosynthetic ability and established genetic modification systems, cyanobacteria are essential for fundamental and biotechnological research. Till now, hundreds of cyanobacterial genomes have been sequenced, and transcriptomic analysis has been frequently applied in the functional genomics of cyanobacteria. However, the massive omics data have not been extensively mined and integrated. Here, we describe CyanoOmicsDB (http://www.cyanoomics.cn/), a database aiming to provide comprehensive functional information for each cyanobacterial gene. CyanoOmicsDB consists of 8 335 261 entries of cyanobacterial genes from 928 genomes. It provides multiple gene identifiers, visualized genomic location, and DNA sequences for each gene entry. For protein-encoding genes, CyanoOmicsDB can provide predicted gene function, amino acid sequences, homologs, protein-domain super-families, and accession numbers for various public protein function databases. CyanoOmicsDB integrates both transcriptional and translational profiles of Synechocystis sp. PCC 6803 under various environmental culture coditions and genetic backgrounds. Moreover, CyanoOmicsDB includes 23 689 gene transcriptional start sites, 94 644 identified peptides, and 16 778 post-translation modification sites obtained from transcriptomes or proteomes of several model cyanobacteria. Compared with other existing cyanobacterial databases, CyanoOmicsDB comprises more datasets and more comprehensive functional information. CyanoOmicsDB will provide researchers in this field with a convenient way to retrieve functional information on cyanobacterial genes.

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