Sequence Analysis of the Genome of Carnation (Dianthus caryophyllus L.)

The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. ‘Francesco’ was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568 887 315 bp, consisting of 45 088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16 644 bp and 60 737 bp, respectively, and the longest scaffold was 1 287 144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp.     

Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers

Oil-rich seeds of Jatropha curcas are being focussed as a source of bio-diesel. However, prior to its industrial use, a lot of crop improvement efforts are required in Jatropha. Availability of a large number of EST sequences of Jatropha in public domain allow identification of candidate genes for several agronomic characters including oil content in seeds. Here, we have analysed 42,477 ESTs of Jatropha spanning 22.9 Mbp for microsatellites and fatty acid metabolism related sequences. Unigene sequences were built using CAP 3 programme resulted in 12,358 contigs and 5,730 singlets. Nearly, 8 % unigenes showed presence of microsatellites, slightly over-represented compared to their occurrence in ESTs. Most of the microsatellites were either di- or tri-nucleotide repeats, while other categories of tetra-, penta- and hexa-nucleotide repeats together constituted ~4 % of total microsatellites. Assessment of functional relevance of unigenes was carried out using Blast2GO using its default settings. The overall sequence similarity level against sequences in ‘nr’ database was >80 %. A total of 931 sequences that participated in any of the pathways related to fatty acid or lipid metabolism were found at GO level 6. Among these, GO terms “Fatty acid metabolic process” and “Fatty acid biosynthetic process” were most over-represented. Overall, our work has due relevance in identifying molecular markers for the candidate genes for oil content in Jatropha seeds, and will prove to be an important reference for further studies for identification of trait specific markers in Jatropha.     

Intra- specific variation in response of Jatropha (Jatropha curcas L.) to elevated CO2 conditions

Twenty genotypes of Jatropha collected from diverse eco-geographic regions from the states of Chhattisgarh (3), Andhra Pradesh (12), Rajasthan (4) and Uttarakhand (1) of India were subjected to elevated CO₂ conditions. All the genotypes showed significant difference (p < 0.05 and 0.01) in the phenotypic traits in both the environments (elevated and ambient) and genotype x environment interaction. Among the physiological traits recorded, maximum photosynthetic rate was observed in IC565048 (48.8 μmol m⁻² s⁻¹) under ambient controlled conditions while under elevated conditions maximum photosynthetic rate was observed in IC544678 (41.3 μmol m⁻² s⁻¹), and there was no significant difference in the genotype x environment interaction. Stomatal conductance (Gs) emerged as the key factor as it recorded significant difference among the genotypes, between the environments and also genotype x environment interaction. The Gs and transpiration (E) recorded a significant decline in the genotypes under the elevated CO₂ condition over the ambient control. Under elevated CO₂ conditions, the minimum values recorded for Gs and E were 0.03 mmol m⁻² s⁻¹ and 0.59 mmol m⁻² s⁻¹ respectively in accession IC565039, while the maximum values for Gs and E were 1.8 mmol m⁻² s⁻¹ and 11.5 mmol m⁻² s⁻¹ as recorded in accession IC544678. The study resulted in the identification of potential climate ready genotypes viz. IC471314, IC544654, IC541634, IC544313, and IC471333 for future use.     

Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South America and are cultivated worldwide, eggplant (Solanum melongena L.) is indigenous to the Old World and in this respect it is phylogenetically unique. To broaden our knowledge of the genomic nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds termed SME_r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated to be covered by SME_r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.     

Occurrence of Arbuscular Mycorrhizal Fungi in Rhizosphere of Jatropha curcas L. in Arid and Semi Arid Regions of India

A study was conducted to identify common arbuscular mycorrhizal (AM) fungi present in rhizosphere of Jatropha curcas L., an important bio-diesel crop, from different arid and semi arid regions of India viz., Jodhpur (Rajasthan), Hissar (Haryana), Jhansi and Lalitpur (Uttar Pradesh) and Hyderabad (Andhra Pradesh). A total of 20 AM species were recorded, which consisted of two species of Acaulospora and 18 species of Glomus. The highest frequency of occurrence was recorded for Glomus intraradix (100%), followed by Acaulospora scrobiculata (83%), G. etunicatum (50%) and Glomus 1 (50%). Maximum species richness was recorded at Jodhpur, followed by Jhansi, Hissar, Hyderabad and Lalitpur. The results seem to suggest that species richness was more in arid regions as compared to semi arid areas.     

High-frequency plant regeneration from leaf-disc cultures of Jatropha curcas L.: an important biodiesel plant

A simple, high-frequency and reproducible protocol for induction of adventitious shoot buds and plant regeneration from leaf-disc cultures of Jatropha curcas L. has been developed. Adventitious shoot buds were induced from very young leaf explants of in vitro germinated seedlings as well as mature field-grown plants cultured on Murashige and Skoog’s (MS) medium supplemented with thidiazuron (TDZ) (2.27 μM), 6-benzylaminopurine (BA) (2.22 μM) and indole-3-butyric acid (IBA) (0.49 μM). The presence of TDZ in the induction medium has greater influence on the induction of adventitious shoot buds, whereas BA in the absence of TDZ promoted callus induction rather than shoot buds. Induced shoot buds were multiplied and elongated into shoots following transfer to the MS medium supplemented with BA (4.44 μM), kinetin (Kn) (2.33 μM), indole-3-acetic acid (IAA) (1.43 μM), and gibberellic acid (GA₃) (0.72 μM). Well-developed shoots were rooted on MS medium supplemented with IBA (0.5 μM) after 30 days. Regenerated plants after 2 months of acclimatization were successfully transferred to the field without visible morphological variation. This protocol might find use in mass production of true-to-type plants and in production of transgenic plants through Agrobacterium/biolistic-mediated transformation.     

Whole Mitochondrial Genome Sequence of an Indian Plasmodium falciparum Field Isolate

Mitochondrial genome sequence of malaria parasites has served as a potential marker for inferring evolutionary history of the Plasmodium genus. In Plasmodium falciparum, the mitochondrial genome sequences from around the globe have provided important evolutionary understanding, but no Indian sequence has yet been utilized. We have sequenced the whole mitochondrial genome of a single P. falciparum field isolate from India using novel primers and compared with the 3D7 reference sequence and 1 previously reported Indian sequence. While the 2 Indian sequences were highly divergent from each other, the presently sequenced isolate was highly similar to the reference 3D7 strain.     

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.     

麻疯树鲨烯合酶基因SQS的克隆及生物信息学分析

以麻疯树(Jatropha curcas L.)总RNA为模板,根据已报道的鲨烯合酶基因序列设计简并引物,用RACE方法克隆得到麻疯树鲨烯合酶基因全长cDNA,命名为JcSQS。JcSQS全长1609 bp,包含1个1242 bp的开放阅读框,预测麻疯树鲨烯合酶基因编码的蛋白含有413个氨基酸。JcSQS具有鲨烯合酶类的保守结构域,JcSQS 蛋白与蓖麻、柿、木榄等植物中SQS基因编码的氨基酸序列具有高度同源性。这为研究麻疯树萜烯类物质的生物合成和调控机制奠定了基础。     

麻疯树皮的化学成分研究

从麻疯树(Jatrophac curcus L.)的树皮中分离得到12个化合物,经理化常数和波谱鉴定(IR,1H NMR,13C NMR,EI-MS)分别为二十六酸甲酯(1),β-谷甾醇(2),蒲公英萜醇(3),蒲公英甾醇(4),伪蒲公英甾醇(5),curcusones A(6),curcusones B(7),jatropholone A(8),jatropholone B(9),3,3′,4-三甲氧基鞣花酸(10),胡萝卜甙(11),蔗糖(12)。其中化合物1,4,5,10,12为首次从该植物中分离得到。     

Transformation of Jatropha curcas L. for production of larger seeds and increased amount of biodiesel

The development of green energy is important to mitigate global warming. Jatropha (Jatropha curcas L.) is a promising candidate for the production of alternative biofuel, which could reduce the burden on the Earth’s resources. Jatropha seeds contain a large quantity of lipids that can be used to produce biofuel, and the rest of the plant has many other uses. Currently, techniques for plant genetic transformation are extensively employed to study, create, and improve the specific characteristics of the target plant. Successful transformation involves the alteration of plants and their genetic materials. The aim of this study was to generate Jatropha plants that can support biofuel production by increasing their seed size using genes found via the rice FOX-hunting system. The present study improved previous protocols, enabling the production of transgenic Jatropha in two steps: the first step involved using auxins and dark incubation to promote root formation in excised shoots and the second step involved delaying the timing of antibiotic selection in the cultivation medium. Transgenic plants were subjected to PCR analysis; the transferred gene expression was confirmed via RT-PCR and the ploidy level was investigated. The results suggest that the genes associated with larger seed size in Arabidopsis thaliana, which were found using the rice FOX-hunting system, produce larger seeds in Jatropha.     

生物柴油植物黑皂树开发利用研究

能源短缺和环境污染是当前人类社会所面临的巨大挑战,生物柴油的推广和应用是现阶段解决替代燃油的重要途径之一。黑皂树种子油是很好的生物柴油原料,目前在许多热带地区大力种植黑皂树。我国华南、西南地区的一些干旱荒地可以种植黑皂树。我们对黑皂树油在柴油机上的应用研究证明:黑皂树油在气温35℃条件下,可以直接在各种柴油机上起动和应用;黑皂树油中掺入20%的轻柴油,其黏度大大降低,冷机起动性能和热效率等均与轻柴油相当。因此,黑皂树油的应用比目前国外使用的生物柴油更经济,是一种很有发展前途的能源植物。     

木本油料植物麻疯树的研究进展

近来,麻疯树(Jatropha curcas L.)因可以作为生物柴油的原料而受到广泛关注。虽然麻疯树具有含油量高且可在边际土地种植的优势,但同时存在理想品种缺乏、种植面积限制、基础研究薄弱等方面的问题。为了使常规育种和生物技术改良工作者更好地了解麻疯树的研究进展,确定日后麻疯树育种和遗传改良的方向,综述了麻疯树种质资源与遗传多样性分析、生理及对环境适应性、组学研究、油脂合成功能基因研究、育种等方面国内外的最新进展。     

Somatic embryogenesis in Jatropha curcas Linn., an important biofuel plant

Jatropha curcas L. is one potential source of non-edible biofuel-producing energy crop. Its importance also lies in its medicinal properties. The species is primarily propagated through heterozygous seeds, and thus the seed oil content varies from 4 to 40%. Moreover, due to its perennial nature, seed setting requires 2 to 3 years time. The seed viability and rate of germination are low, and quality seed screening is another laborious task; thus, seed propagation alone cannot provide quality planting material for sustainable use. Somatic embryogenesis, a powerful tool of plant biotechnology for faster and quality plant production has been successfully applied to regenerate plants in Jatropha curcas for the first time. Embryogenic calli were obtained from leaf explants on MS basal medium supplemented with only 9.3 μM Kn. Induction of globular somatic embryos from 58% of the cultures was achieved on MS medium with different concentrations of 2.3–4.6 μM Kn and 0.5–4.9 μM IBA; 2.3 μM Kn and 1.0 μM IBA proved to be the most effective combination for somatic embryo induction in Jatropha curcas. Addition of 13.6 μM adenine sulphate stimulated the process of development of somatic embryos. Mature somatic embryos were converted to plantlets on half strength MS basal medium with 90% survival rate in the field condition. The whole process required 12–16 weeks of culture for completion of all steps of plant regeneration. This protocol of somatic embryogenesis in Jatropha curcas may be an ideal system for future transgenic research.     

Germination responses to temperature and water potential in Jatropha curcas seeds: a hydrotime model explains the difference between dormancy expression and dormancy induction at different incubation temperatures

Background and Aims

Jatropha curcas is a drought-resistant tree whose seeds are a good source of oil that can be used for producing biodiesel. A successful crop establishment depends on a rapid and uniform germination of the seed. In this work we aimed to characterize the responses of J. curcas seeds to temperature and water availability, using thermal time and hydrotime analysis,

Methods

Thermal and hydrotime analysis was performed on germination data obtained from the incubation of seeds at different temperatures and at different water potentials.

Key Results

Base and optimum temperatures were 14·4 and 30 °C, respectively. Approximately 20 % of the seed population displayed absolute dormancy and part of it displayed relative dormancy which was progressively expressed in further fractions when incubation temperatures departed from 25 °C. The thermal time model, but not the hydrotime model, failed to describe adequately final germination percentages at temperatures other than 25 °C. The hydrotime constant, θ_H, was reduced when the incubation temperature was increased up to 30 °C, the base water potential for 50 % germination,Ψ_b(50), was less negative at 20 and 30 °C than at 25 °C, indicating either expression or induction of dormancy. At 20 °C this less negative Ψ_b(50) explained satisfactorily the germination curves obtained at all water potentials, while at 30 °C it had to be corrected towards even less negative values to match observed curves at water potentials below 0. Hence, Ψ_b(50) appeared to have been further displaced to less negative values as exposure to 30 °C was prolonged by osmoticum. These results suggest expression of dormancy at 20 °C and induction of secondary dormancy above 25 °C. This was confirmed by an experiment showing that inhibition of germination imposed by temperatures higher than 30 °C, but not that imposed at 20 °C, is a permanent effect.

Conclusions

This study revealed (a) the extremely narrow thermal range within which dormancy problems (either through expression or induction of dormancy) may not be encountered; and (b) the high sensitivity displayed by these seeds to water shortage. In addition, this work is the first one in which temperature effects on dormancy expression could be discriminated from those on dormancy induction using a hydrotime analysis.     

Degradation of phorbol esters by Pseudomonas aeruginosa PseA during solid-state fermentation of deoiled Jatropha curcas seed cake

Large amount of seed cake is generated as by-product during biodiesel production from Jatropha seeds. Presence of toxic phorbol esters restricts its utilization as livestock feed. Safe disposal or meaningful utilization of this major by-product necessitates the degradation of these phorbol esters. The present study describes the complete degradation of phorbol esters by Pseudomonas aeruginosa PseA strain during solid state fermentation (SSF) of deoiled Jatropha curcas seed cake. Phorbol esters were completely degraded in nine days under the optimized SSF conditions viz. deoiled cake 5.0 g; moistened with 5.0 ml distilled water; inoculum 1.5 ml of overnight grown P. aeruginosa; incubation at temperature 30 °C, pH 7.0 and RH 65%.SSF of deoiled cake seems a potentially viable approach towards the complete degradation of the toxic phorbol esters.     

麻疯树小孢子发育的研究

用透射电镜观察了麻疯树(Jatropha curcas L.)小孢子发育的超微结构。小孢子母细胞时期内质网和质体较多;减数分裂和四分体时期,细胞处于明显的代谢活跃状态,细胞器丰富,主要有内质网、线粒体、质体、高尔基体和球状体;在小孢子发育早期和晚期,线粒体和内质网仍较丰富;小孢子经过高度的不对称分裂后,形成较大的营养细胞和较小的生殖细胞,营养细胞中细胞器数量明显减少,含大量的淀粉和脂类物质,生殖细胞中脂类物质丰富;表皮、药室内壁和中层细胞在小孢子母细胞和四分体时期淀粉粒丰富,小孢子时期明显减少,绒毡层从小孢子母细胞至小孢子发育晚期的细胞器都很丰富,主要为内质网、质体和线粒体,为二胞花粉发育奠定基础。