Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies

Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We used a staggered mock community to estimate the optimal threshold for species detection. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are diversity estimates, species abundance, and ability of reconstructing de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct-even partially-the metagenome

Deformation history of the blueschist-facies sequences from the Villa de Cura unit (Northern Venezuela)

The Serrania del Interior terrane is located in Northern Venezuela, that represents the southern margin of the Caribbean plate. This terrane includes the Villa de Cura unit, which mainly consists of multiple sub-units of metamorphosed and deformed Cretaceous volcano-sedimentary sequences. These sequences are commonly interpreted as generated in a supra-subduction zone setting. The structural history of the Villa de Cura blueschists-facies units includes four main deformational phases, from D1 to D4. The first D1 phase is mainly represented by a relict S1 schistosity developed under HP/LT conditions. The relic S1 schistosity is deformed by isoclinal to subisoclinal F2 folds showing similar geometry. The F2 folds are characterized by a continuous S2 crenulation cleavage developed under greenschist-facies metamorphism. The parallelism between the A2 axes and the related L2 mineral lineations suggests an interpretation of the F2 folds as sheath folds developed during non-coaxial deformation. The kinematic indicators suggest a top-to-W sense of shear for the D2 phase. The D3 phase is distinguished by asymmetric, parallel F3 folds with a S vergence. Finally, the D4 phase consists of F4 open, gentle folds with high-angle to sub-vertical axial planes. The collected data suggest a complex deformation history, characterized by coupling of strike-slip tectonics and shortening during the retrograde evolution of the blueschist-facies sequences

Syn-exhumation coupling of oceanic and continental units along the western edge of the alpine corsica: A review

The Alpine Corsica represents a segment of the Alpine collisional belt. In its western edge, it is characterized by the close association of continental units deformed under high-pressure metamorphic conditions (Lower Units) and oceanic units showing a metamorphism ranging from high-pressure (Schistes Lus-trés Complex) to very low-grade conditions (Upper Units). This paper provides a complete review of the relationships between the continental and oceanic units in selected five areas where the stratigraphic features, deformation history, metamorphic P-T path and tectonic setting are available for each unit. The collected data indicate that the oceanic units occur not only at the top of the continental ones, as generally proposed in the literature, but also intercalated within them. Such relationships were achieved at shallow structural level during the late stage of exhumation, when the continental units were tectonically coupled with the oceanic units which were dragged as slices from the orogenic wedge. The coupling probably occurred immediately before the transition from syn-to post-orogenic geodynamic regime that affected the whole Alpine-Apennine collisional system in the early Oligocene. After the coupling, the stack of oceanic and continental units experienced a further exhumation-related deformation before their final exposure at the surface

Transcriptome analysis of amyloodinium ocellatum tomonts revealed basic information on the major potential virulence factors

The ectoparasite protozoan Amyloodinium ocellatum (AO) is the etiological agent of amyloodiniosis in European seabass (Dicentrarchus labrax) (ESB). There is a lack of information about basic molecular data on AO biology and its interaction with the host. Therefore, de novo transcriptome sequencing of AO tomonts was performed. AO trophonts were detached from infested ESB gills, and quickly becoming early tomonts were purified by Percoll\uae density gradient. Tomont total RNA was processed and quality was assessed immediately. cDNA libraries were constructed using TruSeq\uae Stranded mRNA kit and sequenced using Illumina sequencer. CLC assembly was used to generate the Transcriptome assembly of AO tomonts. Out of 48,188 contigs, 56.12% belong to dinophyceae wherein Symbiodinium microadriaticum had 94.61% similarity among dinophyceae. Functional annotations of contigs indicated that 12,677 had associated GO term, 9005 with KEGG term. The contigs belonging to dinophyceae resulted in the detection of several peptidases. A BLAST search for known virulent factors from the virulence database resulted in hits to Rab proteins, AP120, Ribosomal phosphoprotein, Heat-shock protein70, Casein kinases, Plasmepsin IV, and Brucipain. Hsp70 and casein kinase II alpha were characterized in-silico. Altogether, these results provide a reference database in understanding AO molecular biology, aiding to the development of novel diagnostics and future vaccines

'Candidatus Phytoplasma solani' interferes with the distribution and uptake of iron in tomato

Background: \u2018Candidatus Phytoplasma solani\u2019 is endemic in Europe and infects a wide range of weeds and cultivated plants. Phytoplasmas are prokaryotic plant pathogens that colonize the sieve elements of their host plant, causing severe alterations in phloem function and impairment of assimilate translocation. Typical symptoms of infected plants include yellowing of leaves or shoots, leaf curling, and general stunting, but the molecular mechanisms underlying most of the reported changes remain largely enigmatic. To infer a possible involvement of Fe in the host-phytoplasma interaction, we investigated the effects of \u2018Candidatus Phytoplasma solani\u2019 infection on tomato plants (Solanum lycopersicum cv. Micro-Tom) grown under different Fe regimes. Results: Both phytoplasma infection and Fe starvation led to the development of chlorotic leaves and altered thylakoid organization. In infected plants, Fe accumulated in phloem tissue, altering the local distribution of Fe. In infected plants, Fe starvation had additive effects on chlorophyll content and leaf chlorosis, suggesting that the two conditions affected the phenotypic readout via separate routes. To gain insights into the transcriptional response to phytoplasma infection, or Fe deficiency, transcriptome profiling was performed on midrib-enriched leaves. RNA-seq analysis revealed that both stress conditions altered the expression of a large (> 800) subset of common genes involved in photosynthetic light reactions, porphyrin / chlorophyll metabolism, and in flowering control. In Fe-deficient plants, phytoplasma infection perturbed the Fe deficiency response in roots, possibly by interference with the synthesis or transport of a promotive signal transmitted from the leaves to the roots. Conclusions: \u2018Candidatus Phytoplasma solani\u2019 infection changes the Fe distribution in tomato leaves, affects the photosynthetic machinery and perturbs the orchestration of root-mediated transport processes by compromising shoot-to-root communication

U-Pb zircon geochronology of intrusive rocks from an exotic block in the Late Cretaceous – Paleocene Taraklı Flysch (northern Turkey): Constraints on the tectonics of the Intrapontide suture zone

In the Boyal\u131 area (northern Anatolia), a thick succession of the Early Maastrichtian - Middle Paleocene Tarakl\u131 Flysch crops out. The Tarakl\u131 Flysch represents a foredeep sediment deposited during the final stage of collision between the Sakarya and Istanbul-Zonguldak continental margins, that developed as a consequence of the closure of the Intrapontide oceanic basin. The top of the Tarakl\u131 Flysch is characterized by a level of slide-block in shaly-matrix lithofacies that can be considered as the result of several fast catastrophic events predating the closure of the basin and its deformation. This level consists of slide-blocks surrounded by monomict pebbly-mudstones and pebbly-sandstones. Among the slide-blocks, the biggest one consists of quartz-monzonites and leucocratic granodiorites of Late Permian age (260.8 \ub1 2.2 Ma) dated by zircon LA-ICP-MS method. By comparison with the regional data, the source area of these granitoids can be identified in the Istanbul-Zonguldak terrane. This evidence suggests a new picture for the paleogeographic setting of the ultimate stage of the continental collision between the Istanbul-Zonguldak and the Sakarya continental margins. In this scenario the coarse-grained deposits of the Tarakl\u131 Flysch are supplied by an orogenic wedge, consisting of oceanic units topped by the Istanbul-Zonguldak terrane. This orogenic wedge represented the north side of the foredeep, while the southern one was represented by the still undeformed Sakarya continental margin

A forward genetics approach integrating genome-wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays)

The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29\ua0573 gene models in RILs and to derive 373\ua0769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript\u2013trait correlations. Then, leaf traits were associated with SNPs in a genome-wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript\u2013trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co-expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize

Transcriptomic and metabolomic profiles of Zea mays fed with urea and ammonium

The simultaneous presence of different N-forms in the rhizosphere leads to beneficial effects on nitrogen (N) nutrition in plants. Although widely used as fertilizers, the occurrence of cross connection between urea and ammonium nutrition has been scarcely studied in plants. Maize fed with a mixture of urea and ammonium displayed a better N-uptake efficiency than ammonium- or urea-fed plants (Buoso et al., Plant Physiol Biochem, 2021a; 162: 613\u2013623). Through multiomic approaches, we provide the molecular characterization of maize response to urea and ammonium nutrition. Several transporters and enzymes involved in N-nutrition were upregulated by all three N-treatments (urea, ammonium, or urea and ammonium). Already after 1 day of treatment, the availability of different N-forms induced specific transcriptomic and metabolomic responses. The combination of urea and ammonium induced a prompt assimilation of N, characterized by high levels of some amino acids in shoots. Moreover, ZmAMT1.1a, ZmGLN1;2, ZmGLN1;5, ZmGOT1, and ZmGOT3, as well transcripts involved in glycolysis-TCA cycle were induced in roots by urea and ammonium mixture. Depending on N-form, even changes in the composition of phytohormones were observed in maize. This study paves the way to formulate guidelines for the optimization of N fertilization to improve N-use efficiency in maize and therefore limit N-losses in the environment

Early cretaceous plume–ridge interaction recorded in the band-e-zeyarat ophiolite (North Makran, Iran): New constraints from petrological, mineral chemistry, and geochronological data

The North Makran domain (southeast Iran) is part of the Makran accretionary wedge and consists of an imbricate stack of continental and Neo-Tethyan oceanic tectonic units. Among these, the Band-e-Zeyarat ophiolite consists of (from bottom to top): ultramafic cumulates, layered gabbros, isotropic gabbros, a sheeted dyke complex, and a volcanic sequence. Sheeted dykes and volcanic rocks are mainly represented by basalts and minor andesites and rhyolites showing either normal-type (N) or enriched-type (E) mid-ocean ridge basalt affinities (MORB). These conclusions are also supported by mineral chemistry data. In addition, E-MORBs can be subdivided in distinct subtypes based on slightly different but significant light rare earth elements, Th, Nb, TiO2, and Ta contents. These chemical differences point out for different partial melting conditions of their mantle sources, in terms of source composition, partial melting degrees, and melting depths. U-Pb geochronological data on zircons from intrusive rocks gave ages ranging from 122 to 129 Ma. We suggest that the Band-e-Zeyarat ophiolite represents an Early Cretaceous chemical composite oceanic crust formed in a mid-ocean ridge setting by partial melting of a depleted suboceanic mantle variably metasomatized by plume-type components. This ophiolite records, therefore, an Early Cretaceous plume–ridge interaction in the Makran Neo-Tethys