CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes

Abstract

To understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. We have extended CyanoBase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed RhizoBase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. Both databases focus on the representation and reusability of reference genome annotations, which are continuously updated by manual curation. Domain experts have extracted names, products and functions of each gene reported in the literature. To ensure effectiveness of this procedure, we developed the TogoAnnotation system offering a web-based user interface and a uniform storage of annotations for the curators of the CyanoBase and RhizoBase databases. The number of references investigated for CyanoBase increased from 2260 in our previous report to 5285, and for RhizoBase, we perused 1216 references. The results of these intensive annotations are displayed on the GeneView pages of each database. Advanced users can also retrieve this information through the representational state transfer-based web application programming interface in an automated manner.

Long-Term Acclimation to Iron Limitation Reveals New Insights in Metabolism Regulation of Synechococcus sp. PCC7002

“…Reads were aligned to the genome of Synechococcus sp. PCC7002 build from the Cyanobase (Fujisawa et al, 2013) and further analyzed using TopHat 2.0 mapper software (Trapnell et al, 2009). Alignment metrics were obtained using Picard Tools (http://broadinstitute.…”

“…Expression levels (indicated as fold change; log 2 FC) of genes for each Fe limiting treatment (0.047, 0.47, and 3.83 pM Fe') were normalized to control treatment (36.7 pM Fe') and considered when the FDR of the adjusted P-value was <0.05 and the log 2 FC was >|2|. Supplemental Table S3 contains the list of all genes differentially expressed under the three Fe levels of Fe limitation tested, with their log 2 FC, log 2 CPM, P-value and FDR, as well as their putative function and functional category defined in Cyanobase (Fujisawa et al, 2013).…”

“…Then, these three groups were further investigated based on the classification of genes in functional categories defined in Cyanobase (Fujisawa et al, 2013). The DEG included in the four other groups (Figure 4) represented 5% of the total of DEG and were not included in further analysis.…”

Oxidation of P700 in Photosystem I Is Essential for the Growth of Cyanobacteria

“…PCC 7002 (S. 7002), unlike S. 6803 and S. 7942 (Zhang et al, 2009;Shaku et al, 2015). The S. 7002 genome, like that of S. 7942, includes genes coding for FLV1/3 isozymes but not for FLV2/4 (Fujisawa et al, 2014). The genetic profiles of flv and other genes related to cyanobacterial AEF, including those of S. 7002, S. 6803, and S. 7942, are summarized in Table I We constructed the S. 7002 mutant, Dflv1/3, which lacks the flv1 and flv3 orthologs present in S. 6803 (SYN-PCC7002_A1743 and SYNPCC7002_A1321; Supplemental Fig.…”

“…For S. 6803, we used a Table I. Genetic background of AEF in three cyanobacteria species used in this study Gene homology analyses were performed in Cyanobase (http://genome.microbedb.jp/CyanoBase; Fujisawa et al, 2014). cox, aa 3 -type cytochrome c oxidase; cyd, cytochrome bd-type quinol oxidase; arto, cytochrome b o -type quinol oxidase; ndhD, D subunit of NAD(P)H dehydrogenase.…”