Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus

Background: The Rosaceae family encompasses numerous genera exhibiting morphological diversification in fruit types and plant habit as well as a wide variety of chromosome numbers. Comparative genomics between various Rosaceous genera has led to the hypothesis that the ancestral genome of the family contained nine chromosomes, however, the synteny studies performed in the Rosaceae to date encompass species with base chromosome numbers x = 7 (Fragaria), x = 8 (Prunus), and x = 17 (Malus), and no study has included species from one of the many Rosaceous genera containing a base chromosome number of x = 9. Results: A genetic linkage map of the species Physocarpus opulifolius (x = 9) was populated with sequence characterised SNP markers using genotyping by sequencing. This allowed for the first time, the extent of the genome diversification of a Rosaceous genus with a base chromosome number of x = 9 to be performed. Orthologous loci distributed throughout the nine chromosomes of Physocarpus and the eight chromosomes of Prunus were identified which permitted a meaningful comparison of the genomes of these two genera to be made. Conclusions: The study revealed a high level of macro-synteny between the two genomes, and relatively few chromosomal rearrangements, as has been observed in studies of other Rosaceous genomes, lending further support for a relatively simple model of genomic evolution in Rosaceae

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

Background: Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed function to every single sequence is impracticable. Bioinformatics tools, easy to use and able to provide automatic and reliable annotations at a genomic scale, are necessary and urgent. In this scenario, the Gene Ontology has provided the means to standardize the annotation classification with a structured vocabulary which can be easily exploited by computational methods.Results: Argot2 is a web-based function prediction tool able to annotate nucleic or protein sequences from small datasets up to entire genomes. It accepts as input a list of sequences in FASTA format, which are processed using BLAST and HMMER searches vs UniProKB and Pfam databases respectively; these sequences are then annotated with GO terms retrieved from the UniProtKB-GOA database and the terms are weighted using the e-values from BLAST and HMMER. The weighted GO terms are processed according to both their semantic similarity relations described by the Gene Ontology and their associated score. The algorithm is based on the original idea developed in a previous tool called Argot. The entire engine has been completely rewritten to improve both accuracy and computational efficiency, thus allowing for the annotation of complete genomes.Conclusions: The revised algorithm has been already employed and successfully tested during in-house genome projects of grape and apple, and has proven to have a high precision and recall in all our benchmark conditions. It has also been successfully compared with Blast2GO, one of the methods most commonly employed for sequence annotation. The server is freely accessible at http://www.medcomp.medicina.unipd.it/Argot2Journal Articleinfo:eu-repo/semantics/publishe

Deconstruction of the (Paleo)Polyploid Grapevine Genome Based on the Analysis of Transposition Events Involving NBS Resistance Genes

Plants have followed a reticulate type of evolution and taxa have frequently merged via allopolyploidization. A polyploid structure of sequenced genomes has often been proposed, but the chromosomes belonging to putative component genomes are difficult to identify. The 19 grapevine chromosomes are evolutionary stable structures: their homologous triplets have strongly conserved gene order, interrupted by rare translocations. The aim of this study is to examine how the grapevine nucleotide-binding site (NBS)-encoding resistance (NBS-R) genes have evolved in the genomic context and to understand mechanisms for the genome evolution. We show that, in grapevine, i) helitrons have significantly contributed to transposition of NBS-R genes, and ii) NBS-R gene cluster similarity indicates the existence of two groups of chromosomes (named as Va and Vc) that may have evolved independently. Chromosome triplets consist of two Va and one Vc chromosomes, as expected from the tetraploid and diploid conditions of the two component genomes. The hexaploid state could have been derived from either allopolyploidy or the separation of the Va and Vc component genomes in the same nucleus before fusion, as known for Rosaceae species. Time estimation indicates that grapevine component genomes may have fused about 60 mya, having had at least 40–60 mya to evolve independently. Chromosome number variation in the Vitaceae and related families, and the gap between the time of eudicot radiation and the age of Vitaceae fossils, are accounted for by our hypothesis

A major QTL controlling apple skin russeting maps on the linkage group 12 of 'Renetta Grigia di Torriana'

Background: Russeting is a disorder developed by apple fruits that consists of cuticle cracking followed by the replacement of the epidermis by a corky layer that protects the fruit surface from water loss and pathogens. Although influenced by many environmental conditions and orchard management practices, russeting is under genetic control. The difficulty in classifying offspring and consequent variable segregation ratios have led several authors to conclude that more than one genetic determinant could be involved, although some evidence favours a major gene (Ru). Results: In this study we report the mapping of a major genetic russeting determinant on linkage group 12 of apple as inferred from the phenotypic observation in a segregating progeny derived from 'Renetta Grigia di Torriana', the construction of a 20 K Illumina SNP chip based genetic map, and QTL analysis. Recombination analysis in two mapping populations restricted the region of interest to approximately 400 Kb. Of the 58 genes predicted from the Golden Delicious sequence, a putative ABCG family transporter has been identified. Within a small set of russeted cultivars tested with markers of the region, only six showed the same haplotype of 'Renetta Grigia di Torriana'. Conclusions: A major determinant (Ru_RGT) for russeting development putatively involved in cuticle organization is proposed as a candidate for controlling the trait. SNP and SSR markers tightly co-segregating with the Ru_RGT locus may assist the breeder selection. The observed segregations and the analysis of the 'Renetta Grigia di Torriana' haplotypic region in a panel of russeted and non-russeted cultivars may suggest the presence of other determinants for russeting in apple

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

Abstract Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.Apple genome research at FEM is supported by the research office of the Provincia autonoma di Trento. DJS and ELG acknowledge a grant from the East Malling Trust. Fragaria genomics at EMR is funded by the BBSRC. JMB is supported by a grant by Plant & Food Research's Excellence Programme. Apple genomics at Plant & Food Research is partially supported by the New Zealand Foundation for Research Science and Technology project C06X0812 "Exploiting Opportunities from Horticultural Genomics". Research conducted at IRTA was partly funded by the CONSOLIDER-INGENIO 2010 Program (CSD2007-00036) and project INIA-RTA2007-00063-00-00, both from the Spanish Ministry of Science and Innovation. RosCOS development at OSU/MSU was funded by the National Research Initiative Competitive Grant 2005-35300-15454 of USDA's National Institute of Food and Agriculture.Peer Reviewe

Oral vaccination with heat inactivated Mycobacterium bovis activates the complement system to protect against tuberculosis

Tuberculosis (TB) remains a pandemic affecting billions of people worldwide, thus stressing the need for new vaccines. Defining the correlates of vaccine protection is essential to achieve this goal. In this study, we used the wild boar model for mycobacterial infection and TB to characterize the protective mechanisms elicited by a new heat inactivated Mycobacterium bovis vaccine (IV). Oral vaccination with the IV resulted in significantly lower culture and lesion scores, particularly in the thorax, suggesting that the IV might provide a novel vaccine for TB control with special impact on the prevention of pulmonary disease, which is one of the limitations of current vaccines. Oral vaccination with the IV induced an adaptive antibody response and activation of the innate immune response including the complement component C3 and inflammasome. Mycobacterial DNA/RNA was not involved in inflammasome activation but increased C3 production by a still unknown mechanism. The results also suggested a protective mechanism mediated by the activation of IFN-γ producing CD8+ T cells by MHC I antigen presenting dendritic cells (DCs) in response to vaccination with the IV, without a clear role for Th1 CD4+ T cells. These results support a role for DCs in triggering the immune response to the IV through a mechanism similar to the phagocyte response to PAMPs with a central role for C3 in protection against mycobacterial infection. Higher C3 levels may allow increased opsonophagocytosis and effective bacterial clearance, while interfering with CR3-mediated opsonic and nonopsonic phagocytosis of mycobacteria, a process that could be enhanced by specific antibodies against mycobacterial proteins induced by vaccination with the IV. These results suggest that the IV acts through novel mechanisms to protect against TB in wild boar

HADES RV program with HARPS-N at the TNG GJ 3998: An early M-dwarf hosting a system of super-Earths

Context. Many efforts are currently made to detect Earth-like planets around low-mass stars in almost every extra-solar planet search. M dwarfs are considered ideal targets for Doppler radial velocity searches because their low masses and luminosities make low-mass planets orbiting in these stars' habitable zones more easily detectable than those around higher mass stars. Nonetheless, the frequency statistics of low-mass planets hosted by low-mass stars remains poorly constrained. Aims: Our M-dwarf radial velocity monitoring with HARPS-N within the collaboration between the Global architectures of Planetary Systems (GAPS) project, the Institut de Ciències de l'Espai/CSIC-IEEC (ICE) and the Instituto de Astrofísica de Canarias (IAC) can provide a major contribution to the widening of the current statistics through the in-depth analysis of accurate radial velocity observations in a narrow range of spectral sub-types (79 stars, between dM0 to dM3). Spectral accuracy will enable us to reach the precision needed to detect small planets with a few Earth masses. Our survey will contribute to the surveys devoted to the search for planets around M-dwarfs, mainly focused on the M-dwarf population of the northern emisphere, for which we will provide an estimate of the planet occurrence. Methods: We present here a long-duration radial velocity monitoring of the M1 dwarf star GJ 3998 with HARPS-N to identify periodic signals in the data. Almost simultaneous photometric observations were carried out within the APACHE and EXORAP programs to characterize the stellar activity and to distinguish those due to activity and to the presence of planetary companions from the periodic signals. We ran a Markov chain Monte Carlo simulation and used a Bayesian model selection to determine the number of planets in this system, to estimate their orbital parameters and minimum mass, and to properly treat the activity noise. Results: The radial velocities have a dispersion in excess of their internal errors due to at least four superimposed signals with periods of 30.7, 13.7, 42.5, and 2.65 days. Our data are well described by a two-planet Keplerian (13.7 d and 2.65 d) and a fit with two sinusoidal functions (stellar activity, 30.7 d and 42.5 d). The analysis of spectral indexes based on Ca II H & K and Hα lines demonstrates that the periods of 30.7 and 42.5 days are due to chromospheric inhomogeneities modulated by stellar rotation and differential rotation. This result is supported by photometry and is consistent with the results on differential rotation of M stars obtained with Kepler. The shorter periods of 13.74 ± 0.02 d and 2.6498 ± 0.0008 d are well explained with the presence of two planets, with masses of at least 6.26_(-0.76)^(+0.79) M⊕ and 2.47 ± 0.27 M⊕ and distances of 0.089 AU and 0.029 AU from the host, respectively. -- Based on: observations made with the Italian Telescopio Nazionale Galileo (TNG), operated on the island of La Palma by the INAF - Fundación Galileo Galilei at the Roche de Los Muchachos Observatory of the Instituto de Astrofísica de Canarias (IAC); photometric observations made with the APACHE array located at the Astronomical Observatory of the Aosta Valley; photometric observations made with the robotic telescope APT2 (within the EXORAP program) located at Serra La Nave on Mt. Etna. http://www.oact.inaf.it/exoit/EXO-IT/Projects/Entries/2011/12/27_GAPS.html</A

VizieR Online Data Catalog: GJ 3998 RVs, S and Halpha indexes (Affer+, 2016)

In this table we report the observing log for the GJ3998 spectra and the radial velocities, S, and Hα indexes. The star GJ3998 has been monitored from BJD=2456439.6 (26 May 2013) to BJD=2457307.8 (12 October 2015). We obtained a total of 136 data points spanning 869-days. The spectra were obtained at high resolution (R=115000) with the optical echelle spectrograph HARPS-N with exposure times of 15 minutes and an average signal-to-noise ratio (S/N) of 45 at 5500Å. Of the 136 epochs, 76 were obtained within the GAPS time and 60 within the Spanish time. Observations were gathered without the simultaneous Th-Ar calibration, which is commonly used to correct for instrumental drifts during the night. The M-type stars of the HADES program were observed by the Italian team in conjunction with other GAPS targets, which used the Th-Ar simultaneous calibration, therefore we estimated the drift data between the two fibers (star and reference calibration) for each night from these observations and evaluated the interpolated drift for GJ3998 (0.7m/s). Data reduction and spectral extraction were performed using the Data Reduction Software (DRS, Lovis & Pepe, 2007A&A...468.1115L, Cat. J/A+A/468/1115). RVs were measured by means of a weighted cross-correlation function (CCF) with the M2 binary mask provided with the DRS. The RVs were also measured by matching the spectra with a high S/N template obtained by coadding the spectra of the target, as implemented in the TERRA pipeline (Anglada-Escude & Butler, 2012ApJS..200...15A, Cat. J/ApJS/200/15), which provides a better RV accuracy when applied to M dwarfs. We list the observation dates (barycentric Julian date or BJD), the signal-to-noise ratios (S/Ns), the radial velocities (RVs) from the DRS and TERRA pipelines (indicated with a T) and the Hα and S indexes, calculated both by the TERRA pipeline and by an independent method described in the text. The RV errors reported are the formal ones and do not include the jitter term. The S index and Hα errors are calculated as described in the text and do not take into account the photon noise. The S index and Hα errors derived from the TERRA pipeline are due to photon noise through error propagation. (1 data file)

Evidence for the 125 GeV Higgs boson decaying to a pair of tau leptons

Peer reviewe