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Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development.

Alagna F, D'Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G - BMC Genomics (2009)

Bottom Line: Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface.Massively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development.Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNR-Institute of Plant Genetics, Via Madonna Alta 130, 06128 Perugia, Italy.

ABSTRACT

Background: Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits.

Results: Fruits of Coratina, a widely cultivated variety characterized by a very high phenolic content, and Tendellone, an oleuropein-lacking natural variant, were used as starting material for monitoring the transcriptome. Four different cDNA libraries were sequenced, respectively at the beginning and at the end of drupe development. A total of 261,485 reads were obtained, for an output of about 58 Mb. Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface.

Conclusion: Massively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development. Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.

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Depiction of enzyme-encoding TCs grouped by classes, each describing the main enzymatic activity. (A). B and C represent TCs encoding enzymes involved in biosynthesis of plant metabolites and lipids, respectively. The number of TCs encoding each enzyme class is reported on the x axis of each graph.
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Figure 4: Depiction of enzyme-encoding TCs grouped by classes, each describing the main enzymatic activity. (A). B and C represent TCs encoding enzymes involved in biosynthesis of plant metabolites and lipids, respectively. The number of TCs encoding each enzyme class is reported on the x axis of each graph.

Mentions: TCs and sESTs coding for enzymes with assigned EC number were 5,040 and 5,864, respectively (Figure 4A) following the ENZYME classification scheme . The majority of the enzyme-related unigenes encode for transferases (3,982), hydrolases (2,628) and oxidoreductases (1,895). Of particular relevance for fruit metabolism are those TCs and sESTs involved in the biosynthesis of secondary metabolites (761) and lipids (1,005) (Figure 4B, C). Most frequently, the same enzymatic function is redundantly encoded by several unigenes, this may be the result of different proteins referenced with the same EC number or the effect of different transcripts encoding specific enzyme subunits. Given the limited sequence length typically provided by 454 pyrosequencing, it is also plausible that in some cases different TCs and sESTs cover non-matching fragments of the enzyme transcript coding frame.


Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development.

Alagna F, D'Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G - BMC Genomics (2009)

Depiction of enzyme-encoding TCs grouped by classes, each describing the main enzymatic activity. (A). B and C represent TCs encoding enzymes involved in biosynthesis of plant metabolites and lipids, respectively. The number of TCs encoding each enzyme class is reported on the x axis of each graph.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2748093&req=5

Figure 4: Depiction of enzyme-encoding TCs grouped by classes, each describing the main enzymatic activity. (A). B and C represent TCs encoding enzymes involved in biosynthesis of plant metabolites and lipids, respectively. The number of TCs encoding each enzyme class is reported on the x axis of each graph.
Mentions: TCs and sESTs coding for enzymes with assigned EC number were 5,040 and 5,864, respectively (Figure 4A) following the ENZYME classification scheme . The majority of the enzyme-related unigenes encode for transferases (3,982), hydrolases (2,628) and oxidoreductases (1,895). Of particular relevance for fruit metabolism are those TCs and sESTs involved in the biosynthesis of secondary metabolites (761) and lipids (1,005) (Figure 4B, C). Most frequently, the same enzymatic function is redundantly encoded by several unigenes, this may be the result of different proteins referenced with the same EC number or the effect of different transcripts encoding specific enzyme subunits. Given the limited sequence length typically provided by 454 pyrosequencing, it is also plausible that in some cases different TCs and sESTs cover non-matching fragments of the enzyme transcript coding frame.

Bottom Line: Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface.Massively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development.Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNR-Institute of Plant Genetics, Via Madonna Alta 130, 06128 Perugia, Italy.

ABSTRACT

Background: Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits.

Results: Fruits of Coratina, a widely cultivated variety characterized by a very high phenolic content, and Tendellone, an oleuropein-lacking natural variant, were used as starting material for monitoring the transcriptome. Four different cDNA libraries were sequenced, respectively at the beginning and at the end of drupe development. A total of 261,485 reads were obtained, for an output of about 58 Mb. Raw sequence data were processed using a four step pipeline procedure and data were stored in a relational database with a web interface.

Conclusion: Massively parallel sequencing of different fruit cDNA collections has provided large scale information about the structure and putative function of gene transcripts accumulated during fruit development. Comparative transcript profiling allowed the identification of differentially expressed genes with potential relevance in regulating the fruit metabolism and phenolic content during ripening.

Show MeSH