190 research outputs found
The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants
No full textNext generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger sequencing. As of today, only three research groups working in plant sciences have exploited this potentiality. They showed that pooled NGS can provide results in excellent agreement with those obtained by individual Sanger sequencing. Aim of this review is to convey to the reader the general ideas underlying the use of pooled NGS for the identification of rare variants. To facilitate a thorough understanding of the possibilities of the method we will explain in detail the variations in study design and discuss their advantages and disadvantages. We will show that information on allele frequency obtained by pooled next generation sequencing can be used to accurately compute basic population genetics indexes such as allele frequency, nucleotide diversity and Tajima’s D. Finally we will discuss applications and future perspectives of the multiplexed NGS approach
Structural variation and genome complexity: is dispensable really dispensable?
No full textStructural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) substantially contribute to genetic variation and have an important effect on phenotypic diversity. Since unbalanced SVs are by definition sequences present only in some individuals, they have therefore been referred to as dispensable genome and are not necessary for survival, even though they may provide an important contribution to phenotypic diversity within the species. However, some multi-copy sequences of the dispensable genomes (e.g., multigene families) may be needed in a given proportion by each individual, thus belonging to a conditionally dispensable portion of the pan-genome. Another interesting aspect reported by recent studies is that the rate at which SVs are formed might be influenced by the mating system and by common environmental stresses. In conclusion the dispensable genome plays an important role in genome evolution and in the complex interplay between the genome and the environment
Estimates of genetic and environmental contribution to 43 quantitative traits support sharing of a homogeneous environment in an isolated population from South Tyrol, Italy.
No full textAs part of the genomic health care program 'GenNova', we measured 43 quantitative traits in 1,136 subjects living in three isolated villages in South Tyrol (Italy), for which extended genealogical information was available. Thirty-seven of the studied traits had been previously investigated in other populations, while six of them are, to the best of our knowledge, studied here for the first time. For all 43 traits we estimated narrow-sense heritability, individual-specific environmental effects, and shared environmental effects. Estimates of narrow-sense heritability were in good agreement with previous findings. We found significant heritability for all traits; after correcting for multiple testing, all traits except serum concentration of glutamic oxaloacetic transaminase (GOT) and potassium still showed significant heritability. In contrast, the effect of living in the same sibship or village (the so-called sibship and household effects, respectively) was significant for a few traits only, and after correcting for multiple testing no trait showed significant shared environment effect. We suggest that the sharing of a highly similar environment by the subjects included in this study explains the low contribution of the household effects to the overall trait variation. This peculiarity should provide an advantage in gene-mapping projects by reducing environmental bias
Metamorphic evolution of the Saka Unit (Central Pontides, Northern Turkey): new implications for the Mesozoic convergence-related processes in the Intra-Pontide suture zone
No full textIn Northern Turkey, the Intra-Pontide suture (IPS) zone represents an east-west trending belt of deformed and/or metamorphic rocks bounded by the Istanbul-Zonguldak Terrane (IZ) to the north and the Sakarya Composite Terrane (SK) to the south (e.g. Göncüoğlu et al., 1997). Despite its importance for the geodynamics reconstructions of the Black Sea and Eastern Mediterranean areas during the Mesozoic, the IPS zone has been poorly investigated; only recently the role of its metamorphic units during the syn-collisional evolution was explored (Marroni et al., 2014; Frassi et al., 2016; 2017)
In order to provide new insights on the Mesozoic-Tertiary geodynamic reconstruction of the southern margin of the Laurasia, we present new data from the Saka Unit from the eastern portion of the IPS. Using a multidisciplinary approach that includes lithological, structural, metamorphic and petrographic investigations, we constrained the P-T-t path during the Mesozoic subduction and consequent exhumation and accretion to Laurasia. Following the determination of mesostructures, we analysed a series of samples of metabasite and metapelite. Mineral chemistry of phases at equilibrium in the pervasive S2 foliation was determined, and PT determinations were performed through pseudosection calculation of three samples. PT conditions are within the epidote-amphibolite facies, with pressures of 1.2 ± 0.15 GPa and Temperatures 600 ± 50 °C, thus higher than those determined previously, suggesting that S2 could be a composite foliation where a progressive evolution acquired during onset of exhumation was recorded. A comparison with the PT evolutions of the nearby Daday and Domuz-Dag units, shows that they record lower T at D2 at different ages, and that the pre-D2 conditions, when they are preserved, are different in the three units.
References
Frassi C., Göncüoğlu M.C., Marroni M., Pandolfi L., Ruffini L. Ellero A., Ottria G. & Sayit K. 2016. The Intra-Pontide Suture Zone in the Tosya-Kastamonu area, Northern Turkey. J. of Maps. 12, 211-219
Frassi, C, Marroni, M., Pandolfi, L., Göncüoğlu, M. C., Ellero, A., Ottria, G., Sayit, K., McDonald, C.S., Balestrieri, M.L. & Malasoma, A. 2018. Burial and exhumation history of the Daday Unit (Central Pontides, Turkey): implications for the closure of the Intra-Pontide oceanic basin. Geol. Mag., 155, 356-376.
Göncüoğlu, M. C., Marroni, M., Sayit, K., Tekin, U. K., Ottria, G., Pandolfi, L. & Ellero, A., 2012. The Ayli Dag ophiolite sequence (central-northern Turkey): A fragment of middle Jurassic oceanic lithosphere within the Intra-Pontide suture zone. Ofioliti, 37, 77–91.
Marroni, M., Frassi, C., Göncüoğlu, C. M., Di Vincenzo, G., Pandolfi, L., Rebay, G., Ellero, A. & Ottria, G. 2014. Late Jurassic amphibolite-facies metamorphism in the Intra-Pontide Suture Zone (Turkey): an eastward extension of the Vardar Ocean from the Balkans into Anatolia? J. Geol. Soc., 171, 605–608
Phloem-restricted phytoplasmas impair carbon fixation in tomato
No full textPhytoplasmas are prokaryotic obligated parasites of plants
that colonize the sieve elements of their host plant, causing
alterations in phloem function such as occlusion, nutrients
uptake and utilization, impairment of photosynthesis and
photo assimilates translocation. Symptoms have been well
described and include inhibition and decline of photosynthesis
efficiency and alterations in sugar metabolism. Our
research group has been investigating the effects of ‘Candidatus
Phytoplasma solani’ infection on tomato plants (Solanum
lycopersicum cv. Micro-Tom) by RNA-sequencing.
Analyzing tomato plants grown under different Fe regimes,
we demonstrated that infection changes Fe distribution in
leaves, affects photosynthetic machinery and perturbs shootto-
root communication. Moreover, infection impacts mineral
nutrient fluxes and alters ion homeostasis of K, Ca, Mg, Fe
and Mn. Here, we focus our analysis on the transcriptional
regulation of genes involved on carbon fixation and carbon
metabolism. A gene co-expression network was investigated
with a weighted correlation approach implemented in the
R package WGCNA. Gene expression and protein analysis
highlighted key genes of carbon fixation pathway and confirmed
impairment of carbon metabolism
Environmental methane emissions from seagrass wrack and evaluation of salinity effect on microbial community composition
No full textMethane generation from seagrass contributes to green-house gases emissions but can also be a potential controlled biogas source. Understanding the natural fluctuations of emissions and the biotic and abiotic factors underlying such variations is essential. In this work, CH4 emission from beach-cast seagrass from the High-Adriatic coast was analysed. Biochemical methane potential (BMP) tests were used to evaluate CH4 generation at different temperatures (30 °C and 35 °C) and salinity levels (from 0‰ to 35‰), consistent with the typical observed environmental conditions. The changes in the microorganism community composition were investigated by means of amplicon metagenomics sequencing. The results underlined a specific CH4 emission in the range of 0.90–1.37 NmL CH4/g Volatile Solids (VS) d at 35 °C and 0.36–0.50 NmL CH4/g VS d at 30 °C. The most intense methane generation was observed at intermediate salinity levels of 18‰ at 35 °C and 9‰ at 30 °C. The total seasonal emission from the investigated beach-cast seagrass was estimated as 0.1399 mmol CH4/m2g. The microbial community analysis highlighted that Rhodobacteraceae was the most abundant family, coherently with its abundance in the marine environment. Low salinity (0–9‰) samples showed a prevalence of carbohydrate–degrading Ruminococcaceae, while the carbohydrate-fermenting Petrotogaceae were more abundant in high salinity (18–35‰) samples. The total lack of an important functional class was not noticed in any salinity level, except for sulphate-reducing bacteria, which were virtually absent when salinity was 0‰. The present study allows a better understanding of the environmental conditions resulting in a higher methanogenic potential and an enhanced comprehension of the bacterial communities associated to this process. The obtained information can be of help for designing efficient systems for producing methane from seagrass wrack, as well as for selecting the most appropriate managing route among the currently available technologies (such as on-site environmental preservation, composting, anaerobic digestion)
Biological weighting function of the UV-B-induced impairment of phototaxis in the freshwater ciliate Ophryoglena flava.
No full textWe determined the biological weighting function (BWF) of the effect of UV radiation on phototaxis of the freshwater, histophagous ciliate Ophryoglena flava. Dose-effect curves were measured by exposing the cells to 12 different irradiation regimens obtained with two different levels of UV-B radiation and by using six filters with cutoff wavelengths ranging from 280 to 335 nm. The results show that there are significant damages to phototaxis at the doses used and that the effect increases when the cutoff is shifted toward short wavelengths. The data were used to calculate the BWF of phototaxis impairment by applying a nonlinear fit procedure. The BWF thus obtained decays exponentially with increasing wavelength in agreement with similar findings reported in the literature for other systems
A Metabarcoding Approach to Investigate Fungal and Oomycete Communities Associated with Kiwifruit Vine Decline Syndrome in Italy
No full textSince 2012, kiwifruit vine decline syndrome (KVDS) has severely compromised all major kiwifruit-growing areas in Italy. Thus far, etiological studies were mainly focused on waterlogging effects or on the isolation of microorganisms from diseased plants; therefore, an all-encompassing picture of KVDS microbiota is still missing. This work aims to describe oomycete and fungal communities associated with KVDS and to identify key taxa potentially involved in the disease through a metabarcoding approach on root endosphere and rhizosphere samples. Two nearby fields with similar pedoclimatic conditions were identified based on KVDS spreading during a 4-year survey (2016 to 2019). In total, four sampling areas were selected, one from the control field with no sign of KVDS (asymptomatic site) and three from the KVDS-affected field (diseased site): (i) asymptomatic until the sampling date in 2018, (ii) symptomatic since 2018, and (iii) symptomatic since 2017. Total genomic DNA samples were subjected to a nested PCR approach separately targeting the internal transcribes spacer 2 regions of fungal and oomycete communities. The communities were compared in terms of α- and β-diversities, and key taxa were identified using univariate differential abundance tests. Major differences in taxa distribution were observed between samples from the different sites (asymptomatic and diseased) and were mostly linked to the oomycete community. Phytophthora sojae was the main taxa characterizing the diseased site and supposed to be involved in the disease and Phytopythium spp. were found related to the different plant health status. Finally, Dactylonectria macrodidyma, Phytopythium citrinum, and Thielaviopsis basicola were also proposed as new KVDS-related pathogens
- …
