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Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds.

Natarajan P, Kanagasabapathy D, Gunadayalan G, Panchalingam J, Shree N, Sugantham PA, Singh KK, Madasamy P - BMC Genomics (2010)

Bottom Line: This resulted in 7009 unigenes which were annotated by BLASTX.It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins.The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu, 603 203, India.

ABSTRACT

Background: Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs).

Results: A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 10(6) clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes.

Conclusions: The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.

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Distributions of ESTs in Contigs. Assembly of 12,084 ESTs resulted in 2258 contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each contig was ranged between 2 and 23. The contig size represents the number of ESTs in the contig.
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Figure 2: Distributions of ESTs in Contigs. Assembly of 12,084 ESTs resulted in 2258 contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each contig was ranged between 2 and 23. The contig size represents the number of ESTs in the contig.

Mentions: Contig assembly of the 12, 084 ESTs was done to remove the redundant ESTs so that the unique ESTs (unigenes) can be annotated. The summary of the contig assembly is given in Table 1. It showed 2258 contigs and 4751 singletons. The contig size ranged between 2 and 23 (Figure 2) and there were 7333 ESTs in the 2258 contigs indicating the presence of 5075 redundant ESTs. The 2258 contigs were manually checked and the longest EST from each contig was selected as unigene. These representative ESTs from contigs and the 4751 singletons together resulted in 7009 unigenes from the 12,084 ESTs assembled.


Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds.

Natarajan P, Kanagasabapathy D, Gunadayalan G, Panchalingam J, Shree N, Sugantham PA, Singh KK, Madasamy P - BMC Genomics (2010)

Distributions of ESTs in Contigs. Assembly of 12,084 ESTs resulted in 2258 contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each contig was ranged between 2 and 23. The contig size represents the number of ESTs in the contig.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091748&req=5

Figure 2: Distributions of ESTs in Contigs. Assembly of 12,084 ESTs resulted in 2258 contigs comprising 7333 ESTs. The distribution of 7333 ESTs in each contig was ranged between 2 and 23. The contig size represents the number of ESTs in the contig.
Mentions: Contig assembly of the 12, 084 ESTs was done to remove the redundant ESTs so that the unique ESTs (unigenes) can be annotated. The summary of the contig assembly is given in Table 1. It showed 2258 contigs and 4751 singletons. The contig size ranged between 2 and 23 (Figure 2) and there were 7333 ESTs in the 2258 contigs indicating the presence of 5075 redundant ESTs. The 2258 contigs were manually checked and the longest EST from each contig was selected as unigene. These representative ESTs from contigs and the 4751 singletons together resulted in 7009 unigenes from the 12,084 ESTs assembled.

Bottom Line: This resulted in 7009 unigenes which were annotated by BLASTX.It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins.The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, Tamil Nadu, 603 203, India.

ABSTRACT

Background: Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs).

Results: A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 10(6) clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes.

Conclusions: The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.

Show MeSH
Related in: MedlinePlus