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

Abstract

BackgroundDespite 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.ResultsFruits 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.ConclusionMassively 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.

Identification and validation of novel EST-SSR markers in olives

“…In contrast, microsatellite expansion in the 3' UTRs can cause transcription slippage and produce expanded mRNA (Li et al, 2004). An elevated percentage of sequences with no putative function may also only be attributed to specifically evolved gene functions and exclusive characteristics to O. europaea species, as reported by Alagna et al (2009). The analysis of motifs of microsatellites in olive UTRs showed that tri-and di-nucleotides occurred in 35 % and 24 %, respectively.…”

“…Among them, genic microsatellites, or expressed sequence tag-derived simple sequence repeats (EST-SSRs), have found a special place in plant genetics and breeding of several agricultural plants (Kalia et al, 2011;Varshney et al, 2005). However, a few transcriptome projects on the generation of ESTs in olive have been completed recently (Alagna et al, 2009;Muñoz-Mérida et al, 2013;Ozgenturk et al, 2010;Rešetič et al, 2013), and a limited number of EST-SSRs are currently available in olives (Adawy et al, 2015;De la Rosa et al, 2013;Essalouh et al, 2014). The main purpose of this study was to increase the number of validated EST-SSRs, for the benefit of all interested research groups, via the identification of simple sequence repeats (SSRs) from the transcripts of developing olive fruits of the variety "Istrska belica".…”

The difference between Treg cells and naive T cells analyzed by cluster analysis

“…Many instructions and tools are available to biologists using their RNA-seq data. RNA-seq more fully reveals the biological individuals at specific times and specific tissue global gene expression [5][6][7][8][9] , such as the discovery of new transcripts. [10] Gene chip is a traditional method for detecting differences in gene expression.…”

Bioinformatics Applied to Proteomics

“…Even in full sequenced genomes, such as in Arabidopsis or humans, this deep sequencing is allowing to identify new transcripts not present in previous ESTs collections (Weber et al, 2007;Sultan et al, 2010). Also specific transcriptomes are being generated in species for which previous genomic resources lacked because of the large size of their genomes (Alagna et al, 2009;Wang et al, 2009;Craft et al, 2010) The new transcripts are also being used for microarrays design (Bellin et al,2009), and also for high throughput SSRs or SNPs identification. SNP detection is performed by aligning raw reads from different genotypes to a reference genome or transcriptome previously available in plants (Barbazuk et al, 2006), as in plants, (Trick et al, 2009;Guo et al, 2010), animals (Satkoski et al, 2008) and humans (Nilsson et al, 2004).…”