Development of KaPPA-View4 for omics studies on Jatropha and a database system KaPPA-Loader for construction of local omics databases

Abstract

Abstracte publication of the whole genome sequence of Jatropha curcas L. has contributed to the study of gene functions of this plant, especially in data-driven investigations such as transcriptome and proteome analyses. Metabolomics analyses of Jatropha have also been reported in recent years. However, the analytical tools for omics data from Jatropha are limited. We prepared a set of pathway maps where the predicted genes of Jatropha were assigned based on KEGG pathway maps, and developed an omics viewer named KaPPA-View4-Jatropha where the pathway maps were implemented. Out of 40,929 predicted genes, 8085 genes were mapped on the KEGG Metabolism maps, other KEGG maps, or gene category maps that were generated from gene classi cation data of KEGG BRITE. Two transcriptome datasets, four metabolome datasets and one gene co-expression dataset were registered in the viewer. To facilitate data sharing of unpublished omics data among research collaborators, we developed a local database system, KaPPA-Loader. ese data mining environments and the supporting database system will help Jatropha researchers to discover key genes such as those involved in oil production, biosynthesis of toxic compounds, and stress resistance. KaPPA-View4-Jatropha and KaPPA-Loader are available from the KaPPA-View portal site (http://kpv.kazusa.or.jp/).

Improvement of physical, chemical and biological properties of aridisol from Botswana by the incorporation of torrefied biomass

“…To stabilize the metabolic activities and microbial variations in soils, they were incubated in a chamber at 25 °C and 10% moisture for 1 month and sampled twice a week. Seeds of J. curcas IP2P accession 39 were germinated in 0.8 wt% agar gel with no nutrients as described in a previous study 40 . The germinated seeds after 10 days of growth were transplanted into the matured soils using quadruplicate experiments for the control and 1%, 3%, and 5% of torrefied biomass.…”

Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

“…Here we present a workflow for a metabolomics study of Jatropha curcas L. [ 59 , 60 ], a biofuel plant, to illustrate an example of the practical use of the KOMICS resources ( Figure 5 ). LC-Orbitrap-MS analyses were conducted using 4 developmental stages of J. curcas fruit samples.…”

JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants

“…The current database release contains a total of 25,297 genes and 33,785 transcripts, including protein-coding genes (22,446, about 89%), non-coding genes (2391, about 9%), and TUCP genes (460, about 2%). Compared with existing J. curcas databases [13, 15, 32], JCDB includes more non-coding genes and more annotation information, as well as unique gene networks and expression profiles (Table 2). In JCDB, about 58, 40, and 74% of genes have GO, KEGG, and Pfam annotations, respectively; there are also about 90% genes in the co-expression network, 38% genes in the PPI network, and 114 expression profiles for 25,297 genes.…”

“…Advances in J. curcas research have led to the creation of several J. curcas genetic information resources. For instance, the Jatropha Genome Database (JAT_r4.5) focuses on the J. curcas genome sequence and annotation [13], and KaPPA-View4 is a KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway viewer for J. curcas [32]. Although each of these resources provides valuable information, there is a lack of database unification and integration of the J. curcas genome and transcriptome with a broad set of multi-omics analysis results, such as gene functional annotation, gene expression matrices, and gene interaction networks.…”