Genetic Dissection of Disease Resistance to the Blue Mold Pathogen, \u3cem\u3ePeronospora tabacina\u3c/em\u3e, in Tobacco

Tobacco blue mold, caused by the obligately biotrophic oomycete pathogen Peronospora tabacina D.B. Adam, is a major foliar disease that results in significant losses in tobacco-growing areas. Natural resistance to P. tabacina has not been identified in any variety of common tobacco. Complete resistance, conferred by RBM1, was found in N. debneyi and was transferred into cultivated tobacco by crossing. In the present study, we characterized the RBM1-mediated resistance to blue mold in tobacco and show that the hypersensitive response (HR) plays an important role in the host defense reactions. Genetic mapping indicated that the disease resistance gene locus resides on chromosome 7. The genetic markers linked to this gene and the genetic map we generated will not only benefit tobacco breeders for variety improvement but will also facilitate the positional cloning of RBM1 for biologists

Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data

Background The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. Results We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Conclusion Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA

Extensive phenotypic diversity in the cultivated Florist’s Gloxinia, Sinningia speciosa (Lodd.) Hiern, is derived from the domestication of a single founder population

The process of domestication often involves a complex genetic structure with contributions from multiple founder populations, interspecific hybridization, chromosomal introgressions, and polyploidization events that occurred hundreds to thousands of years earlier. These complex origins complicate the systematic study of the sources of phenotypic variation. The Florist's Gloxinia, Sinningia speciosa (Lodd.) Hiern, was introduced into cultivation in England two hundred years ago from botanical expeditions that began in the 18th century. Since that time, amateur plant breeders and small horticultural companies have developed hundreds of cultivars with a wide range of flower colors and shapes. In our genetic study of S. speciosa, we examined an extensive diversity panel consisting of 115 individuals that included different species, wild representatives, and cultivated accessions. Our analysis revealed that all of the domesticated varieties are derived from a single founder population that originated in or near the city of Rio de Janeiro in Brazil. We did not detect any major hybridization or polyploidization events that could have contributed to the rapid increase in phenotypic diversity. Our findings, in conjunction with other features such as a small, low\u2010complexity genome, ease of cultivation, and rapid generation time, makes this species an attractive model for the study of genomic variation under domestication

Proximity effects at ferromagnet-superconductor interfaces

We study proximity effects at ferromagnet superconductor interfaces by self-consistent numerical solution of the Bogoliubov-de Gennes equations for the continuum, without any approximations. Our procedures allow us to study systems with long superconducting coherence lengths. We obtain results for the pair potential, the pair amplitude, and the local density of states. We use these results to extract the relevant proximity lengths. We find that the superconducting correlations in the ferromagnet exhibit a damped oscillatory behavior that is reflected in both the pair amplitude and the local density of states. The characteristic length scale of these oscillations is approximately inversely proportional to the exchange field, and is independent of the superconducting coherence length in the range studied. We find the superconducting coherence length to be nearly independent of the ferromagnetic polarization.Comment: 13 Pages total. Compressed .eps figs might display poorly, but will print fin

Incised valley paleoenvironments interpreted by seismic stratigraphic approach in Patos Lagoon, Southern Brazil

<div><p>ABSTRACT: The Rio Grande do Sul (RS) coastal plain area (33,000 km 2 ) had its physiography modified several times through the Quaternary, responding to allogenic and autogenic forcings. The Patos Lagoon covers a significant area of RS coastal plain (10,000 km 2 ), where incised valleys were identified in previous works. About 1,000 km of high resolution (3.5 kHz) seismic profiles, radiocarbon datings, Standard Penetration Test (SPT) and gravity cores were analyzed to interpret the paleoenvironmental evolution as preserved in incised valley infills. Seismic facies were recognized by seismic parameters. The sediment cores were used to ground-truth the seismic interpretations and help in the paleoenvironmental identification. Key surfaces were established to detail the stratigraphical framework, and seismic facies were grouped into four seismic units, which one classified in respective system tracts within three depositional sequences. The oldest preserved deposits are predominantly fluvial and estuarine facies, representing the falling stage and lowstand system tracts. The Holocene transgressive records are dominated by muddy material, mainly represented by estuarine facies with local variations. The transgression culminated in Late Holocene deposits of Patos Lagoon, representing the highstand system tract. The depositional pattern of the vertical succession was controlled by eustatic variations, while the autogenic forcing (paleogeography and sediment supply) modulated the local facies variation.</p></div

Metabolic and miRNA Profiling of TMV Infected Plants Reveals Biphasic Temporal Changes

Plant viral infections induce changes including gene expression and metabolic components. Identification of metabolites and microRNAs (miRNAs) differing in abundance along infection may provide a broad view of the pathways involved in signaling and defense that orchestrate and execute the response in plant-pathogen interactions. We used a systemic approach by applying both liquid and gas chromatography coupled to mass spectrometry to determine the relative level of metabolites across the viral infection, together with a miRs profiling using a micro-array based procedure. Systemic changes in metabolites were characterized by a biphasic response after infection. The first phase, detected at one dpi, evidenced the action of a systemic signal since no virus was detected systemically. Several of the metabolites increased at this stage were hormone-related. miRs profiling after infection also revealed a biphasic alteration, showing miRs alteration at 5 dpi where no virus was detected systemically and a late phase correlating with virus accumulation. Correlation analyses revealed a massive increase in the density of correlation networks after infection indicating a complex reprogramming of the regulatory pathways, either in response to the plant defense mechanism or to the virus infection itself. Our data propose the involvement of a systemic signaling on early miRs alteration