In order to upgrade the genome sequence information of J. curcas L., we integrated de novo assembly of a total of 537 million paired-end reads generated from the Illumina sequencing platform into the current genome assembly which was obtained by a combination of the conventional Sanger method and the Roche/454 sequencing platform. The total length of the upgraded genome sequences thus obtained was 297,661,187 bp consisting of 39,277 contigs. The average and N50 lengths of the generated contigs were 7,579 bp and 15,950 bp, both of which were increased fourfold from the previous genome assembly. Along with genome sequence upgrading, the currently available transcriptome data were collected from the public databases and assembled into 19,454 tentative consensus sequences. Based on a comparison between these tentative consensus sequences of transcripts and the predictions of computer programs, a total of 30,203 complete and partial structures of protein-encoding genes were deduced. The number of genes with complete structures was increased about threefold from the previous genome annotation. By applying the upgraded genome sequence and predicted protein-coding gene information, the number and features of the tandemly arrayed genes, syntenic relations between Jatropha and other plant genomes, and structural features of transposable elements were investigated. The detailed information on the updated J. curcas genome is available at http://www.kazusa.or.jp/jatropha/.

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The 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 classification 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 To facilitate data sharing of unpublished omics data among research collaborators, we developed a local database system, KaPPA-Loader. These 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/).

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The seed oil of jatropha (Jatropha curcas L.) is a source of biodiesel fuel. Although jatropha can grow in semi-arid lands unsuitable for the food production, its oil productivity in such conditions is unsatisfactory at present. Therefore, it is desirable to improve the oil productivity of jatropha even in semi-arid lands by enhancing its drought tolerance. Genetic engineering is promising to dramatically improve plant traits. Although we previously reported a transformation method, which involves wounding of tissue explants in order to increase the chance of Agrobacterium infection, for jatropha, it remains a challenge to enhance the shoot regeneration and root induction processes. Here, we report the generation of three kinds of transgenic jatropha plants in an attempt to improve their drought tolerance. The first one overexpresses the PPAT gene, which encodes an enzyme that catalyzes the CoA biosynthetic pathway; the second overexpresses the NF-YB gene, which encodes a subunit of the NF-Y transcription factor; and the last overexpresses the GSMT and DMT genes, which encode enzymes that catalyze production of glycine betaine. We also report a modified protocol that improves the efficiency of shoot regeneration and root induction in transgenic jatropha plantlets.

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Cultivation of the biofuel plant Jatropha (Jatropha curcas L.) has spread around the world because of its drought resistance, high seed oil content, and adaptability to different environmental conditions. Because of these attributes, Jatropha has the potential to be one of the main resources for next-generation biodiesel fuel. To improve the productivity of Jatropha biomass, it is important to understand the molecular functions of key Jatropha genes, and to modify various agronomic traits of Jatropha via molecular breeding. A reliable and efficient protocol for genetic transformation of Jatropha is a prerequisite for molecular biology research and breeding on this plant. Here, we developed a system in which the herbicide bispyribac sodium salt, which inhibits acetolactate synthase, was used as the selection agent, and a two-point-mutated acetolactate synthase gene (mALS) was used to confer resistance upon transformants. Application of this system significantly improved the efficiency of Agrobacterium tumefaciens-mediated stable transformation of the high-yielding elite Jatropha population, IP-2P. The bispyribac-mALS system was also successfully applied in the Agrobacterium rhizogenes-mediated hairy roots system, which allowed integration of a foreign gene and expression in Jatropha root tissues within 2 weeks. The new protocols described here are powerful tools not only for functional studies on endogenous genes, but also for the molecular breeding of Jatropha to develop elite varieties.

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The use of Jatropha (Jatropha curcas L.) as a source of biofuel has been well-documented. However, the physiological characteristic and growth analysis studies of Jatropha have received considerably lesser attention. In the present study, to confirm the physiological characteristics of Jatropha, we measured the leaf gas exchange characteristics in response to various environmental conditions. Seedlings were grown in 1/5,000 a pots for 2–3 months under greenhouse conditions. Leaf gas exchange rates were measured in a handmade assimilation chamber (26×30×9 cm), in which a fully expanded whole leaf could be set. Based on the leaf gas exchange characteristics, Jatropha was considered to be a C₃ photosynthesis plant. The photosynthetic rate ranged between 10 and 25 µmol m^－2 s^－1 and light saturation generally occurred at 500–1,000 µmol m^－2 s^－1 photon flux densities (PFD), depending on the growth conditions and leaf positions. Leaf conductance and transpiration rates were saturated at 400–1,000 µmol m^－2 s^－1 PFD, also depending on the growth conditions and leaf positions. Maximum rates of transpiration and leaf conductance were 2–6 mmol m^－2 s^－1 and 200–1,200 mmol m^－2 s^－1, respectively, which are very similar to those in C₃ rice plants. Optimum temperature for photosynthesis was approximately at 25–30°C and the maximum rate was 20 µmol m^－2 s^－1. Application of varying vapor pressure difference (from 1 to 3 kPa) did not affect the photosynthetic rate. Photorespiration in Jatropha was 28.5%, which is within the range of typical C₃ plants. Based on the photosynthetic parameters presented in this study, field performance of Jatropha under severe environmental condition is discussed.

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The current focus of Jatropha curcas L. (Euphorbiaceae) research concerns the biodiesel obtained from the seed. However, the plant is an interesting source of biomass, and it has been applied in various ways. The characterization of the different parts of the plant is very important for better use of the residual biomass after oil harvesting. We divided Jatropha samples into seven samples: leaf, stem, bark, xylem, pith, seed coat and kernel, and their characterization was made using two spectroscopic techniques, namely Fourier transform infrared (FTIR) and nuclear magnetic resonance (NMR). Xylem and seed coat accumulate lignin and possibly O-acetyl-4-O-methylglucurono-β-D-xylan hemicellulose. Xylem lignin was richer in syringyl units and seed coat lignin was richer in guaiacyl units. Leaf, pith and bark accumulate cellulose and no O-acetyl-4-O-methylglucurono-β-D-xylan hemicellulose, and the kernel had a low rate of lignocellulose.

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Jatropha curcas L. (Jatropha) is a promising source of renewable bioenergy, since its abundant seed oil can readily be converted into biodiesel. However, industrial use of Jatropha seed oil is problematic; the toxicity of the seeds and oil endangers the oil users and prevents the use of byproducts, such as seed cakes. The most toxic compounds in Jatropha are phorbol esters (PEs), tetracyclic diterpenoids known for their tumor-promoting activity. It is important to utilize a non-toxic accession of Jatropha that lacks PEs in industrial feedstocks. Here, we used an LC-Orbitrap-MS system to characterize the metabolome of seed kernels from PE-containing and PE-free accessions of Jatropha. Among the more than 12,000 metabolites detected, 18 were specific to the PE-containing accession, and most of these appeared to be PEs or derivatives thereof. In contrast, only four ions were specific to the PE-free accession. These results indicate that PE-containing and PE-free Jatropha are broadly similar in their metabolism, but that the PE-containing accessions undergo PE biosynthesis.

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To understand how metabolism changes during fruit ripening in Jatropha curcas L., we performed a non-targeted analysis of metabolites in fruit (the pericarp and developing young seeds) from each maturation stage by means of liquid chromatography-Orbitrap-mass spectrometry, which provides m/z data with approximately 2 ppm precision. The chromatographic data were processed using bioinformatics tools. The total number of metabolites detected decreased substantially with fruit maturation. Self-organizing map (SOM) analysis and metabolite annotation of the ions detected suggested that dynamic metabolic changes occur during fruit maturation. All chromatographic data were deposited in databases accessible by the public.

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Lignins of Jatropha curcas organs were qualitatively and quantitatively characterized by thioglycolic acid, thioacidolysis, and nitrobenzene oxidation methods. The lignin content of the seed coat was 49.4%, and was the highest among various organs of the plant, while the stem had 15.9% lignin, within the range of usual lignin contents of angiosperm trees. Lignin aromatic components of all organs were composed of guaiacyl and syringyl units. Nitrobenzene oxidation indicated that the ratios of syringyl to guaiacyl lignins in the fruit coat and stem were higher than those in other organs. This study provides basic data for the total utilization of J. curcas wood.

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The high oil content of Jatropha (Jatropha curcas L.) seeds makes Jatropha an attractive resource for the production of sustainable bioenergy. However, the Jatropha seed kernels also contain antinutrients and various toxins that persist in the oil and seed cakes and pose a safety risk. Since phorbol esters (PEs) are the major contributor to toxicity, a better understanding of PE biosynthesis is expected to elucidate an effective strategy for the utilization of Jatropha plants. In this study, a Jatropha curcas casbene synthase homolog (JcCSH) with high sequence similarity to casbene synthases (CSs) from Ricinus communis, Euphorbia esula, and Sapium sebiferum was cloned from Jatropha leaf tissue. CS has been hypothesized to catalyze the first step of phorbol biosynthesis. JcCSH encodes a protein that contains a chloroplast transit peptide and a DDXXD motif that is conserved among known terpene cyclases. JcCSH was expressed in seedlings, mature leaves, and the flesh of developing fruits, but not in developing seeds. Our results suggest that JcCSH is widely involved in casbene biosynthesis in various tissues other than seeds.

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