Transcriptome analysis of the oil-rich seed of the bioenergy crop Jatropha curcas L

Costa, Gustavo G.L.; Cardoso, Kelen Cristiane; Del-Bem, Luiz-Eduardo; Lima, Aline Caroline; Cunha, Muciana A S; Campos-Leite, Luciana de; Vicentini, Renato; Papes, Fábio; Moreira, Raquel Capistrano; Yunes, José Andrés; Campos, F. A. P.; Silva, Marcio J. da

doi:10.1186/1471-2164-11-462

Cited by 120 publications

(95 citation statements)

References 21 publications

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“…4l). Contrary to earlier reports in J. curcas (Costa et al 2010;King et al 2011;Natarajan et al 2010;Jiang et al 2012;Xu et al 2011;Chen et al 2011) which focussed primarily on accumulation of oil, our results suggest a complex regulation of oil metabolism, possibly involving a delicate balance between diversion of carbon to lipid biosynthesis and catabolism of storage reserves to meet energy demands during seed maturation in J. curcas. For example, up regulation of transcripts for glyoxylate cycle specific enzymes like malate synthase and gluconeogenesis related enzymes like fructose 1, 6 bisphosphatase and phosphoenolpyruvate carboxykinase in JC3 suggests a possible breakdown of lipids for energy.…”

Section: Transcripts Related To Central Carbon Metabolismcontrasting

confidence: 99%

“…In the current study where JC3 corresponds to mid-to-late maturation stage, all the transcripts associated with lipid biosynthesis were up regulated (Fig. 4m-q), confirming earlier observations (Costa et al 2010;King et al 2011;Jiang et al 2012;Xu et al 2011;Chen et al 2011) made in the same plant. Our results from transcript expression of lipid metabolism related genes also suggest that accumulation of oil could take place simultaneously with its utilisation as the seed matures in J. curcas.…”

Section: Transcripts Related To Lipid Metabolismsupporting

confidence: 91%

“…However, there are questions (Tenenbaum 2008) related to food security if food crops are to be suggested for the production of biofuel. Furthermore, the process of biofuel production should consume less water and be highly energy efficient, starting from the cultivation of related crops to fuel burning in engines (Costa et al 2010). Jatropha curcas offers a viable alternative in this context as it is not used for edible purposes, is grown only as a fencing plant and is well-adapted to varying soil conditions.…”

Section: Introductionmentioning

confidence: 99%

“…A total of 12,084 expressed sequence tags (ESTs), from developing J. curcas seeds were sequenced and they represented genes coding for diverse biological functions (Natarajan et al 2010). Costa et al (2010) reported EST sequencing based identification of genes related to oil accumulation and degradation using developing and germinating seeds of J. curcas. Global gene expression profiles of developing J. curcas seeds revealed key genes involved in the synthesis of storage lipids and proteins (Jiang et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

Chandran

Sankararamasubramanian

Kumar

et al. 2014

Physiol Mol Biol Plants

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Jatropha curcas has been widely studied at the molecular level due to its potential as an alternative source of fuel. Many of the reports till date on this plant have focussed mainly on genes contributing to the accumulation of oil in its seeds. A suppression subtractive hybridization strategy was employed to identify genes which are differentially expressed in the mid maturation stage of J. curcas seeds. Random expressed sequence tag sequencing of the cDNA subtraction library resulted in 385 contigs and 1,428 singletons, with 591 expressed sequence tags mapping for enzymes having catalytic roles in various metabolic pathways. Differences in transcript levels in early and mid-to-late maturation stages of seeds were also investigated using sequence information obtained from the cDNA subtraction library. Seven out of 12 transcripts having putative roles in central carbon metabolism were up regulated in early seed maturation stage while lipid metabolism related transcripts were detected at higher levels in the later stage of seed maturation. Interestingly, 4 of the transcripts revealed putative alternative splice variants that were specifically present or up regulated in the early or late maturation stage of the seeds. Transcript expression patterns from the current study using maturing seeds of J. curcas reveal a subtle balancing of oil accumulation and utilization, which may be influenced by their energy requirements.

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Section: Transcripts Related To Central Carbon Metabolismcontrasting

confidence: 99%

Section: Transcripts Related To Lipid Metabolismsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

Chandran

Sankararamasubramanian

Kumar

et al. 2014

Physiol Mol Biol Plants

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“…Natarajan et al have reported 12,084 ESTs using a normalized cDNA library from developing seeds (Natarajan et al 2010), and Costa et al have reported 13,249 ESTs using non-normalized cDNA libraries from developing and germinating endosperm (Costa et al 2010). In addition to these approaches using the conventional Sanger sequencing method, e orts have been made to accumulate transcriptome data for Jatropha by using a next-generation sequencer.…”

mentioning

confidence: 99%

Upgraded genomic information of <i>Jatropha curcas</i> L.

Hirakawa

Tsuchimoto

Sakai

et al. 2012

Plant Biotechnology

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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. e total length of the upgraded genome sequences thus obtained was 297,661,187 bp consisting of 39,277 contigs. e 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. e number of genes with complete structures was increased about threefold from the previous genome annotation. By applying the upgraded genome sequence and predicted proteincoding 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. e detailed information on the updated J. curcas genome is available at http://www.kazusa.or.jp/jatropha/. Key words:Jatropha curcas, genome sequencing, transcriptome sequences, tentative consensus sequence, tandem gene duplication, database.Jatropha curcas L. is a perennial small tree or large shrub that belongs to the Euphorbiaceae family. J. curcas is endemic to central America but is distributed throughout the tropics and subtropics of Asia and Africa. J. curcas is an important non-edible oilseed crop with great potential for the production of biodiesel fuel. Since J. curcas is an undomesticated plant, its positive attributes in terms of breeding and utilization are not fully understood.In order to accelerate its genetic improvement, it is desirable to understand the genome information of J. curcas. With this goal in mind, we have analyzed the genome sequence of J. curcas by applying combined sequencing methods, and have made the obtained sequence information available through the public and web databases.e accumulated genome information (JAT_r3.0) was 285,858,490 bp consisting of 120,586 contigs and 29,831 singlets, and this accounted for approximately 95% of the gene-containing regions. A total of 40,929 complete and partial structures of proteinencoding genes have been deduced on the accumulated genome sequences. However, the majority of the predicted genes were partially predicted ones as the contig lengths were relatively short in JAT_r3.0. Further improvement of the genome sequence information is therefore needed.Along with the genome sequence approach, several transcriptome analyses have been attempted. Natarajan et al. have reported 12,084 ESTs using...

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Jatropha curcas: Approaches to Engineer Fatty Acid Synthesis and Abiotic Stress Tolerance

Eswaran¹,

Johnson²

2012

Improving Crop Resistance to Abiotic Stress

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Transcriptome analysis of the oil-rich seed of the bioenergy crop Jatropha curcas L

Cited by 120 publications

References 21 publications

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L.

Upgraded genomic information of <i>Jatropha curcas</i> L.

Jatropha curcas: Approaches to Engineer Fatty Acid Synthesis and Abiotic Stress Tolerance

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