About
104
Publications
44,893
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,095
Citations
Publications
Publications (104)
[This corrects the article DOI: 10.1371/journal.pone.0152943.].
Consumers’ choices are mainly based on fruit external characteristics such as the final size, weight, and shape. The majority of edible fruit are by tree fruit species, among which peach is the genomic and genetic reference for Prunus. In this research, we used a peach with a slow ripening (SR) phenotype, identified in the Fantasia (FAN) nectarine,...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa...
The protein IDN2, together with the highly similar interactors FDM1 and FDM2, is required for RNA-directed DNA methylation (RdDM) and siRNA production. Epigenetic regulation of gene expression is required to restrict cell fate determination in A. thaliana ovules. Recently, three transcripts sharing high similarity with the A. thaliana IDN2 and FDM1...
Hypericum perforatum L. (2n = 4x = 32) is an attractive model system for the study of aposporous apomixis. The earliest phenotypic features of aposporous apomixis in this species are the mitotic formation of unreduced embryo sacs from a somatic cell of the ovule nucellus and the avoidance of meiosis. In this research we addressed gene expression va...
Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques to assess the D...
The introgression of apomixis in major seed crops, would guarantee self-seeding of superior heterotic seeds over generations. In the grass species Paspalum simplex, apomixis is controlled by a single locus in which recombination is blocked. In the perspective of isolating the genetic determinants of apomixis, we report data on sequencing, in silico...
The development of F1 hybrid varieties benefits from the synergistic effect of conventional and molecular marker-assisted breeding schemes. A sequencing run was carried out in Foeniculum vulgare (2n=2x=22) to develop the first genome draft and to discover microsatellites suitable for implementing multilocus SSR marker assays. A preliminary cytometr...
Apomixis (asexual reproduction through seeds) is considered a deviation of the sexual reproductive pathway leading to the development of clonal progenies genetically identical to the mother plant. Here we used the Methylation-Sensitive Amplification Polymorphism (MSAP) technique to characterize cytosine methylation patterns occurring in florets of...
Key message
ncRNA PN_LNC_N13 shows contrasting expression in reproductive organs of sexual and apomictic Paspalum notatum genotypes.
Abstract
Apomictic plants set genetically maternal seeds whose embryos derive by parthenogenesis from unreduced egg cells, giving rise to clonal offspring. Several Paspalum notatum apomixis related genes were identif...
Due to growing concern for the genetic erosion of local varieties, four of the main corn landraces historically grown in Veneto (Italy) — Sponcio, Marano, Biancoperla and Rosso Piave — were characterized in this work. A total of 197 phenotypically representative plants collected from field populations were genotyped at 10 SSR marker loci, which wer...
The “Orzo Agordino” is a very old local variety of domesticated barley (Hordeum vulgare subsp. distichum L.) that is native to the Agordo District, Belluno Province, and is widespread in the Veneto Region, Italy. Seeds of this landrace are widely used for the preparation of very famous dishes of the dolomitic culinary tradition such us barley soups...
Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and egg cells, and their autonomous develo...
Radicchio (Cichorium intybus subsp. intybus var. foliosum L.) is one of the most important leaf chicories, used mainly as a component for fresh salads. Recently, we sequenced and annotated the first draft of the leaf chicory genome as we believe it will have an extraordinary impact from both scientific and economic points of view. Indeed, the avail...
The identification and characterization of transcripts involved in flower organ development, plant reproduction and metabolism represent key steps in plant phenotypic and physiological pathways, and may generate high-quality transcript variants useful for the development of functional markers. This study was aimed at obtaining an extensive characte...
Phylogenetic tree of flower organ genes.
Detailed phylogenetic tree of the floral organ identity determinants based on ABC model. The tree was constructed using the Neighbour-Joining method. The p-distance model and the pairwise deletion option were adopted. A bootstrap analysis was performed by using 1,000 replications. Bootstrap values higher tha...
Protein involved in flower development.
Key proteins in flower development according to the ABC model that were included in the phylogenetic analysis.
(DOC)
Genes differentially expressed in post anthesis between Leccino e Frantoio.
List of the differentially expressed transcripts between L7-L10 and F7-F10 and their predicted functional annotation. For each TC, the EST contribution to each genotype or developmental stage is also provided.
(XLSX)
Functional annotation of the unigenes.
A) Percent of unigenes that did or did not match the BLAST hits retrieved from the NCBI databases and their distribution in different plant species. B) Distribution of the unigenes in the following main GO categories: biological processes, cellular component and molecular function.
(TIF)
MapMan overview.
The MapMan overview maps related to Metabolism, Regulatory Network, Cellular response and Transcription show the differences in the transcript levels between the cvs. Frantoio and Leccino flowers at anthesis (stage 7–10).
(TIF)
Primers used for the RT-qPCR analyses.
The primer sequences and amplicon sizes are provided.
(DOC)
Genes differentially expressed in pre anthesis between Leccino and Dolce Agogia.
List of the differentially expressed transcripts between L1-L6 and DA1-DA6 and their predicted functional annotation. For each TC, the EST contribution to each genotype or developmental stage is also provided.
(XLSX)
Olive transcripts in EST collection.
Other olive transcripts identified in the EST collection, putatively involved in ovary abortion and pollen-pistil interactions.
(DOCX)
The MapMan overview maps related to Metabolism, Regulatory Network, Cellular response and Transcription show the differences in the transcript levels between the cvs.
Leccino and Dolce Agogia flowers at pre-anthesis (stages 1–6).
(TIF)
Functional annotation of flower unigenes.
List of all of the olive flower unigenes and their predicted functional annotation. The best hits from the BLASTX search, GO ID, Kegg ID and KO ID are provided.
(XLSX)
Genes differentially expressed between pre and post anthesis.
List of the differentially expressed transcripts between L1-L6 and L7-L10 and their predicted functional annotation. For each TC, the EST contribution to each genotype or developmental stage is also provided.
(XLSX)
Background:
Leaf chicory (Cichorium intybus subsp. intybus var. foliosum L.) is a diploid plant species (2n=18) of the Asteraceae family. The term “chicory” specifies at least two types of cultivated plants: a leafy vegetable, which is highly differentiated with respect to several cultural types, and a root crop, whose current industrial utilizatio...
The Turin Shroud is traditionally considered to be the burial cloth in which the body of Jesus Christ was wrapped after his death approximately 2000 years ago. Here, we report the main findings from the analysis of genomic DNA extracted from dust particles vacuumed from parts of the body image and the lateral edge used for radiocarbon dating. Sever...
The Turin Shroud is traditionally considered the burial cloth in which the body of Jesus Christ was enveloped after his dead about 2000 years ago. Here we report the main findings from the analysis of genomic DNA extracted from dust particles, which were vacuumed from the backside of Turin Shroud
corresponding to internal parts of the body image an...
The
conservation of landraces in Europe is challenging because very often they have already disappeared or cannot be properly identified, which in turn prevents any possibility for their utilization. This work deals with the collection of molecular and historical data to identify and study the original landraces of common buckwheat (Fagopyrum escul...
St. John's wort (Hypericum perforatum L.) is a medicinal plant that produces important metabolites with antidepressant and anticancer activities. Recently gained biological information has shown that this species is also an attractive model system for the study of a naturally occurring form of asexual reproduction called apomixis, which allows clon...
Microalgae provide one of the more promising strategies for the production of renewable biodiesel and liquid fuels. Coupling biodiesel production and wastewater treatment based on the use of microalgae can be an effective approach for achieving sustainable production. Several pilot programs aimed at lipid production are currently working with Acuto...
St. John’s wort (Hypericum perforatum L.) is a medicinal plant species and also an attractive model system for the study of apomixis, despite a lack of genomic and transcriptomic data. We sequenced and annotated its flower transcriptome to provide critical knowledge toward a better understanding of the genetic control of aposporic and sexual reprod...
The Shroud of Turin is a linen cloth almost five square meters in size that wrapped a man afterwards his death following crucifixion after being beaten, scourged and crowned with thorns. It is the most important relic of Christianity because the Catholic tradition identifies such burial cloth with that where the body of Jesus Christ was wrapped bef...
Seed is the key factor of crop productivity. The commercial success of a newly selected cultivar depends not only on its vegetative attributes but also on its ability to produce seeds. Breeding for seed yield and quality requires new sophisticated technologies, such as apomixis, that will allow overcoming the conventional breeding limits. Apomixis...
MicroRNAs (miRNAs) have recently emerged as important regulators of gene expression in plants. Many miRNA families and their targets have been extensively studied in model species and major crops. We have characterized mature miRNAs along with their precursors and potential targets in Hypericum to generate a comprehensive list of conserved miRNA fa...
In this study, we examine the population structure and inbreeding level of the Italian Lipizzan horse breed by means of AFLP fingerprinting and SSR genotyping. A total of 245 AFLP marker alleles were scored across all horses (n=140) living in the Italian Lipizzan stud in 2007, and microsatellite analysis was performed on all mares (n=42) and stalli...
Specific bioinformatic analyses were carried out in peach and olive, starting with the ab initio identification of genes responsible for flower differentiation (‘ABCDE’ genes). The peach MADS-box genes involved in this process, already identified and partially characterized, were used to validate the bioinformatic approach herein adopted using the...
Self-incompatibility is one of the most important barriers adopted by many flowering plants to prevent inbreeding, thus maintaining diversity within species. The elucidation of this reproductive constraint is crucial in olive (Olea europaea L.) because it may help to improve breeding strategies and orchard management. The available literature repor...
A differential display cDNA-AFLP derived technique was used to identify gene transcripts regulated by chromium (Cr) in relation to sulfur (S) nutrition in Brassica juncea. Twelve-day old plants were grown with 200μM sulfate (+S), without sulfate (-S), with 200μM sulfate plus 200μM chromate (+S+Cr), or without sulfate plus 200μM chromate (-S+Cr). Fo...
Zinc (Zn) is an essential element for plant growth and development, but at high levels this metal can become toxic. Hyperaccumulator species are often not suitable for phytoremediation technologies because they need to be fast growing and have high biomass production, such as those of the Populus genus. Comparative genomics studies of poplars subje...
St. John's wort (Hypericum perforatum L., 2n = 4x = 32) is a medicinal plant that produces pharmaceutically important metabolites with antidepressive, anticancer and antiviral activities. It is also regarded as a serious weed in many countries. H. perforatum is furthermore an attractive model system for the study of apomixis. Natural populations of...
A large proportion of mammalian genomes is represented by transposable elements (TE), most of them being long interspersed nuclear elements 1 (LINE-1 or L1). An increased expression of LINE-1 elements may play an important role in cellular stress-related conditions exerting drastic effects on the mammalian transcriptome. To understand the impact of...
Jatropha curcas L. (2n = 2x = 22) is becoming a popular non-food oleaginous crop in several developed countries due to its proposed value in the biopharmaceutical industry. Despite the potentials of its oil-rich seeds as a renewable source of biodiesel and an interest in large-scale cultivation, relatively little is known with respect to plant repr...
We have compared the transcriptomic profiles of microdissected live ovules at four developmental stages between a diploid sexual and diploid apomictic Boechera. We sequenced >2 million SuperSAGE tags and identified (1) heterochronic tags (n = 595) that demonstrated significantly different patterns of expression between sexual and apomictic ovules a...
Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study d...
RT-PCR validation. Results of the validation of 42 genes analyzed by quantitative Real-Time PCR and grouped according to eight different subgroups of expression patterns among the three fruit developmental stages.
List of enzyme names and codes. List of enzyme names, codes and library of the 89 gene sequences tested by quantitative Real-Time PCR.
KEGG map. KEGG pathway for starch and sucrose metabolism (Map:00500) (A) combined with glycolysis and gluconeogenesis (Map:00010) (B). Box colors: blue and green correspond to up-regulated genes between olive stages 1 and 2, and 2 and 3, respectively, whereas red and yellow correspond to down-regulated genes between olive stages 1 and 2, and 2 and...
KEGG map. KEGG pathway related to fatty acid biosynthesis (Map:00061) (A) and metabolism (Map:00071) (B). Box colors: blue and green correspond to up-regulated genes between olive stages 1 and 2, and 2 and 3, respectively, whereas red and yellow correspond to down-regulated genes between olive stages 1 and 2, and 2 and 3, respectively; gray indicat...
List of specific primers used for RT-PCR analysis. List of specific primers designed on the selected key genes for the validation of their expression patterns by Real-Time PCR analysis.
Secondary metabolism enzymes. List of enzymes involved in the biosynthesis and metabolism of secondary metabolites, such as steroids, phenylpropanoids, flavonoids, alkaloids and specific products like caffeine, limonene and pinene.
MAPMAN map. Overview MAPMAN metabolism map showing several constantly and transiently up- and down-regulated genes related to cell wall synthesis and breakdown, fatty acid biosynthesis and lipid breakdown, starch and sucrose metabolism, glycolysis, Calvin cycle and the secondary metabolism (e.g., terpenoids, flavonoids, phenols). Signal colors: blu...
Number and distribution of plant AFLP records (source: PubMed, years 1994–2007).