Version VI of the ESTree db: an improved tool for peach transcriptome analysis (original) (raw)
Related papers
ESTree db: a Tool for Peach Functional Genomics
BMC Bioinformatics, 2005
Background The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. Results The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. Conclusion The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.
Candidate gene database and transcript map for peach, a model species for fruit trees
Theoretical and Applied Genetics, 2005
Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp.
Exploitation of Structural and Functional Genomics Databases for Gene Identification in Peach
Acta Horticulturae, 2007
This research aims at the development of peach as a model genome for the identification, characterization, and cloning of important genes in Rosaceae species. We have constructed an initial physical map for peach. The map is anchored onto the general Primus genetic map and has been integrated with a peach transcript map (http://www.rosaceae.org). Our efforts to exploit the peach genomic databases are focused on two genomic regions of interest: the distal part of linkage group 2 associated with the genes for root-knot nematode resistance and the distal part of linkage group 4 which is important for fruit characters such as freestone and melting flesh. Our approach combines linkage genetic mapping using EST-based genetic markers, localization of the markers on the physical framework, and sequencing the genomic region of interest. Preliminary results illustrate the efficiency of this strategy to facilitate gene discovery in peach.
Tree Genetics & Genomes, 2009
Expressed sequence tag (EST) represents a resource for gene discovery, genome annotation and comparative genomics in plants. ESTs were derived by sequencing clones from five libraries created from two different fruit tissues (skin and mesocarp), at four ripening stages (from post-allegation to post-climacteric) in three different genotypes of peach (OroA, Bolero and Suncrest). A total of 10,847 EST sequences were produced (dataset A); in addition, 21,857 peach ESTs (dataset B) were obtained from public databases. Clustering and assembly of both datasets gave 17,858 unigenes. Analysis of the sequences allowed the assignment of a putative function to 70.8% of the ESTs. In order to define the relationship among fruit tissues transcriptome, a gene ontology analysis was performed. Differences among organs and among different maturation stages of the same organs were identified in organelle, signal transducer and antioxidant activity. A distance matrix of pairwise correlation coefficients analysis was applied between the libraries. Shoot appeared to outgroup and our analysis proved to be an efficient tool to parallel and complement gene expression studies (for example, based on microarray analysis). We conducted an analysis of the frequency of genes putatively involved in the metabolism of some volatiles, which pointed to a predominant presence of those transcripts in the skin. The metabolic pathways of esters and lactones were selected for further isolation and cloning of key genes. The EST database is available at the web site www.itb.cnr.it/estree.
Plant Science, 2006
The transition from pre-climacteric to climacteric phase is a critical step during fruit development. A holistic approach to study this transition has been undertaken using the first available peach microarray (mPEACH1.0) containing about 4800 oligonucleotide probes corresponding to a set of unigenes most of them expressed during the last stages of fruit development. Microarray hybridizations indicated that among the genes present in the microarray slide, 267 and 109 genes are up-and down-regulated, respectively. Genes have been classified according to the TAIR Gene Ontology into three main categories based on cellular localization, molecular function and biological process. Considering the cellular localization, the most significant up-and down-regulated gene products belong to cell wall and chloroplast compartments. Within the molecular function and biological process categories, a dramatic up-regulation has been detected for genes encoding transcription factors and enzymes involved in ethylene biosynthesis and action. A new member of ETR peach family (Pp-ETR2) has been characterized: this gene shows high similarity to Arabidopsis EIN4, tomato Le-ETR4, and strawberry Fa-ETR2. Transition from S3 to S4 is paralleled by changes in expression of 19 genes encoding transcription factors (TFs) belonging to several families including MADS-box, AUX/IAA, bZIP, bHLH, HD, and Myb. Differential expression of genes involved in specific quality traits has also been observed: besides confirming previous data on cell wall-related gene expression, a new pectinmethyl esterase and two new expansins have been identified. Several genes encoding enzymes acting in the isoprenoid biosynthetic pathway appeared to be strongly induced at S3/S4 transition. Among those involved in carotenoid biosynthesis we found also a b-carotene hydroxylase, responsible for the formation of b-cryptoxanthin, the most abundant carotenoid of ripe yellow peaches. #
Isolation and Initial Characterization of cDNAs for mRNAs Regulated during Peach Fruit Development
Peach [ Prunus persica (L.) Batsch] cDNA libraries have been constructed from RNA isolated from immature (30 days after bloom) and ripe fruit. cDNA clones of interest have been identified by differential hybridization among the cDNAs of various peach cultivars or from several stages in fruit development. In addition, several clones were isolated by low stringency hybridizations with oligonucleotides derived from a tomato polygalacturonase cDNA sequence and a cucumber peroxidase amino acid sequence. The pattern of accumulation of the corresponding mRNAs during fruit development was examined by RNA gel-blot analyses in the commercial cultivar Suncrest. Three cDNA clones, pch201, pch307, and pch313, were related to mRNAs that accumulate during the softening stage of fruit development. cDNA clones pchl03, pch205, and pch306 were related to an mRNAs that increase in abundance throughout development, with maximum levels in ripe fruit. cDNA clones pch104 and pch202 were related to mRNAs that exhibit maximum abundance in midfruit development, and clone pch108 was related to mRNA that decreases as the fruit matures. Southern analyses indicated that seven of the cDNAs are represented by only a few genes, while pch104 detects a repetitive family, and pch307 detects a small family of genes. These clones will provide the initial source of genes to manipulate and affect fruit development.
GENE EXPRESSION PROFILE DURING APRICOT FRUIT GROWTH, USING A PEACH MICROARRAY
I International Symposium on Horticulture in Europe, 2009
There is a high degree of sequence conservation within the Family Rosaceae and, in particular, among the Prunus species. The first available peach microarray (µPEACH1.0) was employed for the investigation of the transcription profile during apricot (Prunus armeniaca) fruit growth and development. Fruits (cv. 'Goldrich') were harvested at two growth stages, corresponding to immature (6 weeks before harvest) and ripe (at harvest) stage. Overall, this preliminary transcriptomic approach suggests that peach microarray can be employed in a heterologous fashion. Amongst the 746 genes which could be statistically analysed, 287 were induced, while 260 were down-regulated. In addition to the well documented role of genes implicated in ethylene biosynthesis perception and transduction as well as those involved in cell wall metabolism, this study brings into light a putative role for genes encoding auxin-regulated proteins, and those responsive to stress conditions and to other biotic or abiotic stimuli. The data of the present study can also be used for comparative purposes within Prunus species, since for 203 and 189 genes that were up-and down-regulated respectively during apricot fruit development, data exist for their regulation during the last stages of peach fruit ripening. Future experiments should include analysis of more fruit stages and data validation for the genes of interest. Considering the high degree of sequence conservation within the Family Rosaceae and, in particular, among the Prunus species, the first available peach microarray 113 Proc.
Comparative transcript profiling of a peach and its nectarine
Gene expression at harvest was compared for two stone fruit cultivars, a peach and its near-isogenic nectarine mutant, using two microarray platforms, μPEACH1.0 and ChillPeach. Together, both platforms covered over 6,000 genes out of which 417 were differentially expressed between the fruits of the two cultivars at a p value of 0.05. A total of 47 genes in nectarine and 60 genes in peach were at least twofold higher relative to each other. Nectarine had much better storage characteristics than peach and could be stored for over 5 weeks at 5 °C without storage disorders. In an attempt to determine whether gene expression at harvest could give an indication of storage potential, the expression analysis of the two cultivars was compared to that of two genotypes with different sensitivities to chilling injury. Principal component analysis of gene expression results across four fruit types differing in chilling sensitivity resulted in 41 genes whose expression levels separated the fruits according to sensitivity to storage disorders, suggesting that the genes have a role in cold response adaptation.