ArticleBMC genomics2011
De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 95 citations in OpenAlex.
- Genome-Wide Identification, Expression Patterns and Sugar Transport of the Physic NutInternational journal of molecular sciences · 2022Article
- Genome-Wide Identification and Comparative Analysis ofFrontiers in genetics · 2022Article
- Comparative gene expression profile analysis of ovules provides insights into Jatropha curcas L. ovule development.Scientific reports · 2019Article
- Article
- Genome-wide comparative analysis of papain-like cysteine protease family genes in castor bean and physic nut.Scientific reports · 2018Article
- Transcriptome Analysis Reveals Dynamic Fat Accumulation in the Walnut Kernel.International journal of genomics · 2018Article
- Seed development of Jatropha curcas L. (Euphorbiaceae): integrating anatomical, ultrastructural and molecular studies.Plant cell reports · 2017Article
- Enriching Genomic Resources and Marker Development from Transcript Sequences ofInternational journal of genomics · 2017Article
- Integrated analysis of 454 and Illumina transcriptomic sequencing characterizes carbon flux and energy source for fatty acid synthesis in developingBiotechnology for biofuels · 2017Article
- Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit.BMC genomics · 2016Article
- Unravelling molecular mechanisms from floral initiation to lipid biosynthesis in a promising biofuel tree species, Pongamia pinnata using transcriptome analysis.Scientific reports · 2016Article
- De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia.Functional & integrative genomics · 2016Article
- Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.).Molecular genetics and genomics : MGG · 2016Article
- Genome-Wide Identification of Jatropha curcas Aquaporin Genes and the Comparative Analysis Provides Insights into the Gene Family Expansion and Evolution in Hevea brasiliensis.Frontiers in plant science · 2016Article
- De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis.BMC genomics · 2015Article
- Transcriptome Analysis Comparison of Lipid Biosynthesis in the Leaves and Developing Seeds of Brassica napus.PloS one · 2015Article
- An efficient protocol forPlant biotechnology reports · 2015Article
- Transcriptome of the inflorescence meristems of the biofuel plant Jatropha curcas treated with cytokinin.BMC genomics · 2014Article
- Multi-Spectroscopic Analysis of Seed Quality and 13C-Stable-Iotopologue Monitoring in Initial Growth Metabolism of Jatropha curcas L.Metabolites · 2014Article
- Comparative de novo transcriptome analysis and metabolic pathway studies of Citrus paradisi flavedo from naive stage to ripened stage.Molecular biology reports · 2014Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundJatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier, 10,983 unigenes from Sanger sequencing of ESTs, and 3,484 unique assembled transcripts from 454 pyrosequencing of uncloned cDNAs were reported. In order to expedite the process of gene discovery, we have undertaken 454 pyrosequencing of normalized cDNAs prepared from roots, mature leaves, flowers, developing seeds, and embryos of J. curcas.
resultsFrom 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. De novo contig assembly of these reads generated 17,457 assembled transcripts (contigs) and 54,002 singletons. Average length of the assembled transcripts was 916 bp. About 30% of the transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX analysis revealed that 2,589 of these transcripts are full-length. The assembled transcripts were validated by RT-PCR analysis of 28 transcripts. The results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways including the oil biosynthesis pathway. Overall, the current study reports 14,327 new assembled transcripts which included 2589 full-length transcripts and 27 transcripts that are directly involved in oil biosynthesis.
conclusionThe large number of transcripts reported in the current study together with existing ESTs and transcript sequences will serve as an invaluable genetic resource for crop improvement in jatropha. Sequence information of those genes that are involved in oil biosynthesis could be used for metabolic engineering of jatropha to increase oil content, and to modify oil composition.
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