Candidate gene database and transcript map for peach, a model species for fruit trees (original) (raw)
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Version VI of the ESTree db: an improved tool for peach transcriptome analysis
BMC bioinformatics, 2008
The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features.
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.
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.
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.
Tree Genetics & Genomes, 2010
The goal of the present study was to identify candidate genes (CGs) involved in fruit quality in peach that can be transferred to other Rosaceae species. Two cDNA libraries from fruit of the "Fantasia" peach cultivar, constructed at two stages of development, were used to generate a set of expressed sequence tag sequences. A total of 1,730 peach unigenes were obtained after clustering. Sequences and corresponding annotations were stored in a relational database and are available through a web interface. Fifty-nine CGs involved in fruit growth and development or fruit quality at maturity, focusing on sweetness, acidity, and phenolic compound content, were selected according to their annotation. Fifty-five primer pairs, designed from peach CG sequences and giving PCR products in peach, were tested in strawberry and 36 gave amplified products. Eight CGs were mapped in peach, 14 in strawberry, four in both species and confirmed the pattern of synteny already proposed using comparative mapping. In peach, the CGs are located in three linkage groups (3, 5, 7), and in strawberry they are distributed in all seven Fragaria linkage groups. Colocalization between some of these CGs and quantitative trait loci for fruit quality traits were identified and are awaiting confirmation in further analyses.
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.
BMC Genomics, 2009
Background Cold storage is used to inhibit peach fruit ripening during shipment to distant markets. However, this cold storage can negatively affect the quality of the fruit when it is ripened, resulting in disorders such as wooliness, browning or leathering. In order to understand the individual and combined biological effects that factors such as cold storage and ripening have on the fruit and fruit quality, we have taken a comparative EST transcript profiling approach to identify genes that are differentially expressed in response to these factors. Results We sequenced 50,625 Expressed Sequence Tags (ESTs) from peach mesocarp (Prunus persica O'Henry variety) stored at four different postharvest conditions. A total of 10,830 Unigenes (4,169 contigs and 6,661 singletons) were formed by assembling these ESTs. Additionally, a collection of 614 full-length and 1,109 putative full-length cDNA clones within flanking loxP recombination sites was created. Statistically analyzing the E...
Tree Genetics & Genomes, 2011
Considering the high degree of sequence conservation within the Rosaceae family and, in particular, among the Prunus species, we employed the first available peach oligonucleotide microarray (μPEACH 1.0) for studying the transcriptomic profile during apricot (cv. ‘Goldrich’) fruit development. Apricot fruits were harvested at three distinct developmental stages, corresponding to immature green (6 weeks before fully ripe stage), mature firm ripe (change of peel colour, 1 week before fully ripe stage) and fully ripe, namely T1, T2 and T3, respectively. When applied to μPEACH1.0, apricot target cDNAs showed significant hybridization with an average of 43% of spotted probes, validating the use of μPEACH1.0 to profile the transcriptome of apricot fruit. Microarray analyses carried out separately on peach (cv. ‘Fantasia’) and apricot fruit to profile transcriptome changes during fruit development showed that 70% of genes had the same expression pattern in both species. Such data indicate that the transcriptome is quite similar in apricot and peach fruit and also highlight the presence of species-specific transcript changes. In apricot, 400 and 74 differentially expressed genes were found during the transition from T1 to T2 and from T2 to T3, respectively. Among these, a considerable number of genes encoding IAA protein in action regulators (Aux/IAA) and heat shock proteins (HSPs) were highly up-regulated at early and late ripening, respectively. Intriguingly, the expression profiles of all considered HSPs and some of IAA protein /IAA genes showed different patterns between apricot and peach during the last stages of on-tree fruit development, suggesting the presence of diverse mechanism regulating ripening in these two close phylogenetically related species.
Transcript profiling methods are increasingly used to understand the biological basis of growth and development, and fruit quality in the case of fruits. Such methods provide information for thousands of genes, including those of still unknown function. Furthermore, high-throughput methodologies can be used for comprehensive transcriptome analyses, which may lead to further elucidation of fruit growth and development. Microarray is an attractive genomic tool, since it can be used in a heterologous fashion for gene discovery and characterization in species where few resources are available. In the current study, the progress of apricot (Prunus armeniaca cv. Goldrich) fruit ripening during the last developmental stages was monitored and microarray data that were produced were used for comparative in silico studies with data reported during the transition of peach and nectarine fruits from pre-climacteric to climacteric stage. Transcriptomic studies for both fruit species were carried out using the first available peach microarray (µPEACH 1.0) that contains 4,806 oligonucleotides, each corresponding to a single unigene. Intriguingly, a sharp increase of transcript levels in genes regulating an array of heat shock proteins was detected in apricot fruit, which was not the case during nectarine fruit ripening. In addition, we focused on transcript levels of auxin regulated proteins and their role during the last phases of fruit ripening. Overall, data of the present study offers an initial descriptive picture of transcript profiling of novel key genes and their putative role during the last stages of fruit development is challenged. A future perspective, which will also encompass data validation for genes of interest, is the unravelling of the mechanisms underlying the ripening process in stone-fruits, through the identification of genes differentially expressed during peach and apricot ripening and their correlation with traits of agronomic interest.