De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

<p>Abstract</p> <p>Background</p> <p><it>Jatropha curcas </it>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 <it>J. curcas</it>.</p> <p>Results</p> <p>From 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. <it>De novo </it>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.</p> <p>Conclusion</p> <p>The 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.</p

Optimization of fatty acid determination in selected fish and microalgal oils

The use of ten fatty acid methyl ester reference standards coupled with a detailed quantification method was shown to significantly optimize the fatty acid determination of selected fish and microalgal oils when compared to methods that use only one reference standard (C19:0 or C23:0) as a relative response factor. When using the mixture of ten reference standards after transesterifying oils with NaOH/BF3, determination of total fatty acids, eicosapentaenoic acid and docosahexaenoic acid improved by an average of 7.3, 11.5 and 8.4%, respectively. Furthermore, improvements of 13.9, 18.9 and 6.8% of total fatty acids, EPA and DHA, respectively, were obtained when using the mixture of reference standards for fatty acid determination after directly extracting and transesterifying oil contained in microalgal cells with a mixture of methanol, HCl and chloroform. Fatty acid methyl ester standards dissolved in isooctane showed &lt;5% variability throughout 130 days of stability testing when stored at &minus;20 &deg;C. The optimized method can be used for improving the quantification of fatty acids in both oils (fish and microalgal oils) and dry microalgal cells.<br /