variabilta' genetica ed espressione di elementi retrotrasponibili in girasole (Helianthus annuus L.) e specie affini.

Gli elementi retrotrasponibili sono delle sequenze di DNA capaci di muoversi verso nuovi siti cromosomici. Rappresentano una classe ubiquitaria di sequenze di DNA ripetitivo e costituiscono la maggior parte dei genomi eucarioti. La loro ripetitività nel genoma è riconducibile alla modalità di trasposizione. Si tratta di un meccanismo replicativo basato sulla formazione di un intermedio ad RNA codificante gli enzimi coinvolti nella retrotrascrizione dell’mRNA in copie di cDNA a doppia elica extracromosomico e nell’integrazione di questi in nuovi siti del genoma. Tale meccanismo di trasposizione suggerisce un’origine retrovirale di questi elementi. La classe più frequentemente presente nelle piante superiori è quella dei retrotrasposoni con lunghe ripetizioni terminali (Long Terminal Repeats, LTR) alle estremità 5’ e 3’, i cui membri vengono a loro volta classificati nei due gruppi principali Ty1-Copia e Ty3-Gypsy. Negli ultimi dieci anni lo studio di questi elementi mobili ha consentito lo sviluppo di nuovi ed affidabili strumenti di marcatura molecolare. Ne è un esempio l’IRAP (Inter-Retrotransposon Amplified Polymorphism), una tecnica di DNA fingerprinting basata sull’amplificazione mediante PCR di sequenze comprese fra due retrotrasposoni adiacenti, utilizzando inneschi corrispondenti alle LTR. Tale tecnica è stata applicata per studiare la variabilità genetica in trentasei accessioni selvatiche e in ventisei varianti coltivate di girasole (Helianthus annuus L.) ed in trentanove specie appartenenti al genere Helianthus. Sequenze di DNA corrispondenti a LTR sono state isolate in girasole e su queste sequenze sono stati progettati inneschi corrispondenti a LTR. Gli inneschi sono stati utilizzati in PCR e hanno evidenziato polimorfismi fra i diversi genotipi analizzati. Le accessioni selvatiche di girasole hanno presentato una notevole variabilità, uguale se non superiore a quella rilevata fra le diverse specie del genere Helianthus, spiegabile con la estrema variabilità dell’areale occupato dal girasole selvatico. Al contrario, le varietà coltivate di girasole sono risultate meno variabili. E’ stata poi studiata l’espressione di una famiglia Copia e di tre famiglie Gypsy di retrotrasposoni in embrioni, foglie, fiori e radici di H. annuus, attraverso esperimenti di RT-PCR ed analisi dei polimorfismi con il protocollo IRAP. In letteratura, l’attivazione degli elementi mobili viene di solito riportata in piante esposte a differenti stress. I nostri esperimenti di RT-PCR hanno consentito di verificare la presenza di mRNA delle 4 famiglie analizzate in tutti i tessuti di piante non sottoposte a stress. L’analisi dei polimorfismi ha evidenziato che l’integrazione di nuovi elementi è invece molto rara, suggerendo l’esistenza di meccanismi di silenziamento post-trascrizionale. Nel complesso, i risultati degli esperimenti indicano che i retrotrasposoni sono stati molto attivi durante l’evoluzione del genere Helianthus determinando una grande variabilità genetica sia a livello interspecifico che intraspecifico. I retrotrasposoni di girasole risultano ancora attivi a livello trascrizionale, ma la successiva integrazione di nuovi elementi nel genoma è tenuta strettamente sotto controllo dall’ospite, prevenendo così i rischiosi effetti della retrotrasposizione

Il sistema di garanzia del credito. Effetti sulle PMI.

Le PMI costituiscono il motore dell'economia italiana. Nonostante il ruolo svolto nella promozione della crescita produttiva territoriale, le PMI hanno da sempre maggiori difficoltà nell’ottenere finanziamenti rispetto alle imprese di grandi dimensioni. La principale ragione di ciò può trovare una principale giustificazione nel fatto che le imprese di piccole dimensioni sono più opache, quindi più difficili da valutare per le banche, in quanto offrono bilanci meno dettagliati e minori informazioni. La crisi attuale ha accentuato le difficoltà: in questi ultimi anni le erogazioni nette di prestiti bancari, la principale fonte di finanziamento delle imprese, si sono fortemente ridimensionate. In questo contesto, un ruolo importante può essere giocato dal sistema di garanzia del credito che in Italia è costituito da due componenti: una privata, costituita dai Confidi, e una pubblica, costituita da Fondi Pubblici di Garanzia. In questo lavoro saranno quindi proposte le caratteristiche principali delle due componenti, evidenziandone il ruolo e i cambiamenti normativi degli ultimi anni. Infine, sarà descritto l’impatto di un programma di garanzia pubblico sulle imprese beneficiarie. Il programma è stato attuato dalla Regione Toscana, nel 2009, attraverso Fidi Toscana e prevedeva la costituzione di un Fondo di Garanzia volto a sostenere le imprese che effettuavano investimenti in Toscana e a supportare le imprese a corto di liquidità. La strategia di valutazione adottata si è basata su tecniche di statistica controfattuale, più precisamente sul “propensity-score matching”

Variability in LTR-retrotransposon redundancy and proximity to genes between sunflower cultivars and wild accessions.

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long-terminal-repeat retrotransposons. Being knowledge on the retrotransposon-related variability within this species still limited, we performed a quantitative and qualitative survey of intraspecific variation of LTR-retrotransposon fraction of the genome across different genotypes of H. annuus, using next generation sequencing technologies. First, we characterized the repetitive component of a sunflower homozygous experimental line, using 454 reads, and prepared a library of retrotransposon-related sequences. Then, we analysed the LTRretrotransposon fraction of 7 wild accessions and 8 cultivars of sunflowerby mapping Illumina reads of the 15 genotypes onto the library. We observed large variations in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads of the 15 genotypes onto two sets of sequences, i.e. retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the 15 genomes by counting the number of paired reads of which one mapped onto a retrotransposon and the other onto a gene. Large variability among genotypes was ascertained also for retrotransposonproximity to genes. Both retrotransposon redundancy and proximity to genes showed different behaviour among retrotransposon families and also between cultivated and wild genotypes, indicating a possible involvement in sunflower domestication

A survey of variability in LTR-retrotransposon abundance and proximity to genes between wild and cultivated sunflower genotypes

Sunflower (Helianthus annuus) is an important crop species of the Asteraceae family. Recent characterization of sunflower repetitive fraction has shown that the genome of this species contains a very large proportion of transposable elements, especially long-terminal-repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next generation sequencing technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across different genotypes of H. annuus. First, we characterized the repetitive component of a sunflower homozygous experimental line, using 454 reads, and prepared a library of retrotransposon-related sequences. Then, we analysed the retrotransposon fraction of 7 wild accessions and 8 cultivars of H. annuus by mapping Illumina reads of the 15 genotypes onto the library. We observed large variations in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads of the 15 genotypes onto two sets of sequences, i.e. retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the 15 genomes by counting the number of paired reads of which one mapped onto a retrotransposon and the other onto a gene. Large variability among genotypes was ascertained also for retrotransposon proximity to genes. Both retrotransposon redundancy and proximity to genes showed different behaviour among retrotransposon families and also between cultivated and wild genotypes, indicating a possible involvement in sunflower domestication

Repetitive DNA and plant domestication: variation in copy number and proximity to genes of LTR-retrotransposons among wild and cultivated sunflower (Helianthus annuus) genotypes.

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next generation sequencing technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes - 7 wild accessions and 8 cultivars - of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis we mapped Illumina paired reads to two sets of sequences, i.e. long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was ascertained also for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower

An insight into structure and composition of the fig genome

Ficus carica L. is a diploid species, with a genome size of 0.36 pg/2C, still poorly characterized at genetic and genomic level. With the aim of analysing the fig genome structure, we used Illumina technology to produce 25.64 genome equivalents of 35-511 nt long MiSeq sequences and 12.96 genome equivalents of 25-100 nt long HiSeq paired-end reads. The two libraries were subject to a first assembly run separately, then a hybrid assembly was performed; finally, contigs and supercontigs were scaffolded. This first rough assembly is composed of 264,088 scaffolds, up to 41,760 nt in length, covering 323,708,138 nt, that corresponds to 87.5% of the fig genome, with N50 = 2,523. Masking the scaffolds with a transcriptome of Rosaceae, from which sequences related to repetitive elements were removed, allowed us to establish that coding genes account for at least 6.8% of the fig genome. Gene prediction analysis produced 44,419 putative genes. A sample of around 5,000 predicted genes were annotated with regard to gene ontology and function. Concerning the repetitive component, the fig genome resulted composed for 58.3% of repeated sequences, of which none was especially redundant. Among identified repeats, the most represented were LTR-retrotransposons, with Gypsy elements more frequent than Copia

The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)

Background The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries, but shares numerous morphological and ecological characteristics with F. vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca Findings In this study, the Potentilla micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2,674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of BUSCO genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced Conclusions Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca. The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family

Acute Delta Hepatitis in Italy spanning three decades (1991–2019): Evidence for the effectiveness of the hepatitis B vaccination campaign

Updated incidence data of acute Delta virus hepatitis (HDV) are lacking worldwide. Our aim was to evaluate incidence of and risk factors for acute HDV in Italy after the introduction of the compulsory vaccination against hepatitis B virus (HBV) in 1991. Data were obtained from the National Surveillance System of acute viral hepatitis (SEIEVA). Independent predictors of HDV were assessed by logistic-regression analysis. The incidence of acute HDV per 1-million population declined from 3.2 cases in 1987 to 0.04 in 2019, parallel to that of acute HBV per 100,000 from 10.0 to 0.39 cases during the same period. The median age of cases increased from 27 years in the decade 1991-1999 to 44 years in the decade 2010-2019 (p < .001). Over the same period, the male/female ratio decreased from 3.8 to 2.1, the proportion of coinfections increased from 55% to 75% (p = .003) and that of HBsAg positive acute hepatitis tested for by IgM anti-HDV linearly decreased from 50.1% to 34.1% (p < .001). People born abroad accounted for 24.6% of cases in 2004-2010 and 32.1% in 2011-2019. In the period 2010-2019, risky sexual behaviour (O.R. 4.2; 95%CI: 1.4-12.8) was the sole independent predictor of acute HDV; conversely intravenous drug use was no longer associated (O.R. 1.25; 95%CI: 0.15-10.22) with this. In conclusion, HBV vaccination was an effective measure to control acute HDV. Intravenous drug use is no longer an efficient mode of HDV spread. Testing for IgM-anti HDV is a grey area requiring alert. Acute HDV in foreigners should be monitored in the years to come