CyanoBase: a large-scale update on its 20th anniversary

The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface for large genomic data to include the use of semantic web technologies and JBrowse and have extended community-based reannotation resources through the re-annotation of Synechocystis sp. PCC 6803 by the cyanobacterial research community. These updates have markedly improved CyanoBase, providing cyanobacterial genome annotations as references for cyanobacterial research.

[1]  J. Waterbury,et al.  Generic assignments, strain histories, and properties of pure cultures of cyanobacteria , 1979 .

[2]  Y. Nakamura,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement). , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[3]  Sayaka,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[4]  Takakazu Kaneko,et al.  CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803 , 1998, Nucleic Acids Res..

[5]  Takakazu Kaneko,et al.  CyanoBase: The Genome Database for Synechocystis sp. strain PCC6803 , 1996 .

[6]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[7]  Naoki Sato,et al.  CyanoClust: comparative genome resources of cyanobacteria and plastids , 2010, Database J. Biol. Databases Curation.

[8]  Takakazu Kaneko,et al.  CyanoBase: the cyanobacteria genome database update 2010 , 2009, Nucleic Acids Res..

[9]  Matt Nolan,et al.  Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing , 2012, Proceedings of the National Academy of Sciences.

[10]  Anthony Bretaudeau,et al.  CyanoLyase: a database of phycobilin lyase sequences, motifs and functions , 2012, Nucleic Acids Res..

[11]  Rodrigo Lopez,et al.  Assembly information services in the European Nucleotide Archive , 2013, Nucleic Acids Res..

[12]  Takakazu Kaneko,et al.  CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes , 2013, Nucleic Acids Res..

[13]  C. Tyler-Smith,et al.  Ancient DNA and the rewriting of human history: be sparing with Occam’s razor , 2016, Genome Biology.

[14]  R. Castenholz.  General Characteristics of the Cyanobacteria , 2015 .

[15]  Deanna M. Church,et al.  Assembly: a resource for assembled genomes at NCBI , 2015, Nucleic Acids Res..

[16]  M. Hernández-Prieto,et al.  The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803 , 2016, Scientific Reports.

[17]  Suzanna E Lewis,et al.  JBrowse: a dynamic web platform for genome visualization and analysis , 2016, Genome Biology.