A5016818732- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Plant Disease Resistance and Genetics
- Phytochemistry and biological activities of Ficus species
- Banana Cultivation and Research
- Plant Virus Research Studies
- Plant Pathogens and Resistance
- Plant Pathogenic Bacteria Studies
- Legume Nitrogen Fixing Symbiosis
- Plant Physiology and Cultivation Studies
- Plant nutrient uptake and metabolism
- Genetic diversity and population structure
- Plant Molecular Biology Research
- Sunflower and Safflower Cultivation
- Nematode management and characterization studies
- Berry genetics and cultivation research
- Wheat and Barley Genetics and Pathology
- Mycorrhizal Fungi and Plant Interactions
- Plant Taxonomy and Phylogenetics
- Plant Gene Expression Analysis
- Plant Reproductive Biology
- Agricultural Science and Fertilization
- Evolution and Genetic Dynamics
- Plant Stress Responses and Tolerance
- Marine and coastal plant biology
University of Pisa
2016-2025
Due to DNA heterozygosity and repeat content, assembly of non-model plant genomes is challenging. Herein, we report a high-quality genome reference one the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single-molecule, real-time sequencing. The ~333 Mbp in size, which 80% has been anchored 13 chromosomes. Genome-wide analysis N6 -methyladenine N4 -methylcytosine revealed high methylation levels both genes transposable elements, prevalence methylated over...
The WUSCHEL-related homeobox (WOX) is a family of specific transcription factors involved in plant development and response to stress, characterized by the presence homeodomain. This study represents first comprehensive characterization WOX member Asteraceae family, sunflower (H. annuus L.). Overall, we identified 18 putative HaWOX genes divided phylogenetic analysis three major clades (i.e., ancient, intermediate, WUS). These showed conserved structural functional motifs. Moreover, has...
Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches evaluate the repetitive component of sunflower, by using medium/low coverage Illumina or 454 libraries. By varying technology (Illumina 454), (0.55 x-1.25 x), assemblers assembly procedures, six genomic databases were produced. The annotation these showed that they composed...
Genome divergence by mobile elements activity and recombination is a continuous process that plays key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to same genus still limited. Considering importance Helianthus, model system for studying ecological genetics speciation adaptation, we performed comparative analysis repetitive genome fraction across ten one subspecies sunflower, focusing long terminal repeat...
The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. micrantha a species does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. an attractive choice for comparative genomics studies F. vesca.In this study, genome was sequenced annotated, RNA-Seq data from different developmental stages flowering fruiting were used set gene predictions. A 327 Mbp sequence...
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 (NGS) technologies to perform quantitative and qualitative survey intraspecific variation retrotransposon fraction across 15 genotypes—7 wild accessions 8 cultivars—of H. annuus. By mapping Illumina reads...
In this study, we produced a haplotype-phased genome sequence of the fig tree (Ficus carica L.), non-Rosaceae fruit model species, providing systematic overview organization heterozygous diploid and, for first time in tree, evidence allelic expression direction-shifting among haplotypes. The was used whole analysis heterozygosis, cytosine methylation, and profiles peel pulp tissues. two pseudo-haplotypes spanned approximately 355 346 Mbp, respectively, 97% sequences were associated with 13...
Although Ficus carica L. (fig) is one of the most resistant fruit tree species to salinity, no comprehensive studies are currently available on its molecular responses salinity. Here we report a transcriptome analysis F. cv. Dottato exposed 100 mM sodium chloride for 7 weeks, where RNA-seq was performed leaf samples at 24 and 48 days after beginning salinization; genome-derived fig used as reference. At day 24, 224 transcripts were significantly up-regulated 585 down-regulated, while 48, 409...
Fig trees (Ficus carica L.) are commonly grown in the Mediterranean area, where salinity is an increasing problem coastal areas. Young, fruiting plants of cv. Dottato were subjected to moderate salt stress (100 mM NaCl added irrigation water) for 48 days before fruit sampling. To clarify effect stress, we investigated changes transcription main sugar metabolism-related genes involved synthesis, accumulation and transport soluble carbohydrates ripe fruits by quantitative real-time PCR as well...
Abstract Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R. occidentalis), red idaeus), R. chingii, but very few genomic resources exist blackberries their relatives Rubus. Here we present a chromosome-length assembly annotation of diploid blackberry germplasm accession “Hillquist” argutus). is only known source...
Retrotransposon expression during arbuscular mycorrhizal (AM) fungal colonisation of sunflower roots (Helianthus annuus) was analysed using Illumina RNA-Seq, in order to verify whether symbiosis can activate retrotransposable elements. cDNA libraries were produced from RNAs isolated the plants at 4 and 16 days after inoculation with AM fungus Rhizoglomus irregulare their respective control plants. reads mapped a library reverse transcriptase-encoding sequences, putatively belonging long...
We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa Phaseolus vulgaris) one monocot (Oryza sativa). Retroposition was considered modest importance for formation in all investigated species except V. which showed an unusually high number retro-pseudogenes non coding genic regions. By using a pipeline classification sequence duplicates genomes, we compared relative whole genome, tandem,...
Transposable element activity can be harmful to the host’s genome integrity, but it also provide selective advantages. One strategy cope with transposons is epigenetic control through DNA base modifications. We report non-canonic modification dynamics of fig (Ficus carica L.) by exploiting high-quality reference and related N4-methylcytosine (4mC) N6-methyladenine (6mA) data. Overall, 1.49% transposon nucleotides showed either 4mC or 6mA modifications: 4mC/6mA ratio was similar in Class I II...
The relationship between variation of the repetitive component genome and domestication in plant species is not fully understood. In previous work, variations abundance proximity to genes long terminal repeats (LTR)-retrotransposons sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars wild accessions. this study, we annotated characterized 22 specific retrotransposon families whose varies domesticated genotypes. These mostly belonged Chromovirus...
The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, repertoire predicted genes Japanese cultivar fig (Ficus carica L.) was released. Because the great phenotypic variability that can be found in this species, we decided to study another genotype, Italian cv. Dottato, order perform comparative studies between two cultivars and extend pan genome species. We isolated, sequenced assembled genomic DNA from young fruits Dottato. Then, putative...
Two different methods of calculating insertion profiles long terminal repeat (LTR) retrotransposons in the genome are compared, analysing six retrotransposon lineages Populus trichocarpa. The first method consists aligning two repeats an element and translating nucleotide differences into years, based on synonymous substitution rate. second infers proliferation time profile a group by pairwise genetic distances between reverse transcriptase (RT)-encoding sequences that belong to paralogous...