A Computational Pipeline for the Development of Comparative Anchor Tagged Sequence (CATS) Markers

Key points: Molecular markers that allow the transfer of map information from one species to another are vital in comparative genetics. To identify potential anchor marker sequences more efficiently, we have established a bioinformatic pipeline that combines multi-species EST- and genome- sequence data. Taking advantage of information from a few related species, comparative EST sequence analysis identifies evolutionary conserved sequences in less well-characterised species in the same family. Alignment of evolutionary conserved EST sequences with corresponding genomic sequences defines sets of PCR primer sites flanking introns. Markers identified by this procedure will be readily transferable to other species since they are selected on the basis of their common evolutionary origin. We exemplify our procedure on legumes and grasses, where model plant studies and the genome- and EST-sequence data available have a potential impact on breeding crop species

FX UMa: A New Heartbeat Binary System with Linear and Non-linear Tidal Oscillations and delta Sct Pulsations

We present a detailed analysis of an eclipsing double-lined binary FX UMa based on TESS photometry and newly acquired spectroscopic observations. The radial velocities and atmospheric parameters for each component star are obtained from the SONG high-resolution spectra. Combined with the radial-velocity measurements, our light-curve modeling yields absolute masses and radii of the two components. The Fourier amplitude spectrum of the residual light curve reveals a total of 103 frequencies with signal-to-noise ratio (S/N) > 4, including 12 independent frequencies, 17 multiples of the orbital frequency (Nforb), and 74 combination frequencies. Ten Nforb peaks with S/N > 10 have very high amplitudes and are likely due to tidally excited oscillations (TEOs). The remaining Nforb peaks (4 < S/N < 10) may be originated from the imperfect removal, or they are actually real TEOs. Four anharmonic frequencies can pair up and sum to give exact harmonics of the orbital frequency, suggesting the existence of non-linear tidal processes in the eccentric binary system FX UMa. Eight independent frequencies in the range of 20 to 32 day$^{-1}$ are typical low-order pressure modes of delta Scuti pulsators.Comment: 15+4 pages, 8 figures, Submitted to AJ

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool

<p>Abstract</p> <p>Background</p> <p>Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.</p> <p>Results</p> <p>We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa.</p> <p>Conclusion</p> <p>GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments. The application is available at the greengenes website <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p

MASCARA-2 b: A hot Jupiter transiting the mV=7.6m_V=7.6 A-star HD185603

In this paper we present MASCARA-2 b, a hot Jupiter transiting the $m_V=7.6$ A2 star HD 185603. Since early 2015, MASCARA has taken more than 1.6 million flux measurements of the star, corresponding to a total of almost 3000 hours of observations, revealing a periodic dimming in the flux with a depth of $1.3\%$. Photometric follow-up observations were performed with the NITES and IAC80 telescopes and spectroscopic measurements were obtained with the Hertzsprung SONG telescope. We find MASCARA-2 b orbits HD 185603 with a period of $3.474119^{+0.000005}_{-0.000006}~\rm{days}$ at a distance of $0.057 \pm 0.006~\rm{AU}$, has a radius of $1.83 \pm 0.07~\rm{R}_{\rm{J}}$ and place a $99\%$ upper limit on the mass of $< 17~\rm{M}_{\rm{J}}$. HD 185603 is a rapidly rotating early-type star with an effective temperature of $8980^{+90}_{-130}~\rm{K}$ and a mass and radius of $1.89^{+0.06}_{-0.05}~M_\odot$, $1.60 \pm 0.06~R_\odot$, respectively. Contrary to most other hot Jupiters transiting early-type stars, the projected planet orbital axis and stellar spin axis are found to be aligned with $\lambda=0.6 \pm 4^\circ$. The brightness of the host star and the high equilibrium temperature, $2260 \pm 50~\rm{K}$, of MASCARA-2 b make it a suitable target for atmospheric studies from the ground and space. Of particular interest is the detection of TiO, which has recently been detected in the similarly hot planets WASP-33 b and WASP-19 b.Comment: 8 pages, 4 figures, Accepted for publication in A&

Can legume systeny be useful in guiding the introgression of wild genes into cultivated peanut?

Edição dos resumos do Workshop, Porto Alegre, RS, 2007

Can legume synteny be useful in guiding the introgression of wild genes into cultivated peanut?

Edição do International Workshop Integrating Genomics Into Plant Breeding, Porto Alegre, out. 2007

Suppression of inhomogeneous broadening in rf spectroscopy of optically trapped atoms

We present a novel method for reducing the inhomogeneous frequency broadening in the hyperfine splitting of the ground state of optically trapped atoms. This reduction is achieved by the addition of a weak light field, spatially mode-matched with the trapping field and whose frequency is tuned in-between the two hyperfine levels. We experimentally demonstrate the new scheme with Rb 85 atoms, and report a 50-fold narrowing of the rf spectrum

Solar-like oscillations in γ\gamma Cephei A as seen through SONG and TESS

Fundamental stellar parameters such as mass and radius are some of the most important building blocks in astronomy, both when it comes to understanding the star itself and when deriving the properties of any exoplanet(s) they may host. Asteroseismology of solar-like oscillations allows us to determine these parameters with high precision. We investigate the solar-like oscillations of the red-giant-branch star $\gamma$ Cep A, which harbours a giant planet on a wide orbit. We did this by utilising both ground-based radial velocities from the SONG network and space-borne photometry from the NASA TESS mission. From the radial velocities and photometric observations, we created a combined power spectrum, which we used in an asteroseismic analysis to extract individual frequencies. We clearly identify several radial and quadrupole modes as well as multiple mixed, dipole modes. We used these frequencies along with spectroscopic and astrometric constraints to model the star, and we find a mass of $1.27^{+0.05}_{-0.07}$ M$_\odot$, a radius of $4.74^{+0.07}_{-0.08}$ R$_\odot$, and an age of $5.7^{+0.8}_{-0.9}$ Gyr. We then used the mass of $\gamma$ Cep A and our SONG radial velocities to derive masses for $\gamma$ Cep B and $\gamma$ Cep Ab of $0.328^{+0.009}_{-0.012}$ M$_\odot$ and $6.6^{+2.3}_{-2.8}$ M$_{\rm Jup}$, respectively.Comment: 17 pages, 13 figures, accepted for publication in A&

Precise radial velocities of giant stars XV. Mysterious nearly periodic radial velocity variations in the eccentric binary ϵ\epsilon Cygni

Using the Hamilton Echelle Spectrograph at Lick Observatory, we have obtained precise radial velocities (RVs) of a sample of 373 G- and K-giant stars over more than 12 years, leading to the discovery of several single and multiple planetary systems. The RVs of the long-period (~53 years) spectroscopic binary $\epsilon$ Cyg (HIP 102488) are found to exhibit additional regular variations with a much shorter period (~291 days). We intend to improve the orbital solution of the $\epsilon$ Cyg system and attempt to identify the cause of the nearly periodic shorter period variations, which might be due to an additional substellar companion. We used precise RV measurements of the K-giant star $\epsilon$ Cyg from Lick Observatory, in combination with a large set of RVs collected more recently with the SONG telescope, as well as archival data sets. Our Keplerian model to the RVs characterizes the orbit of the spectroscopic binary to higher precision than achieved previously, resulting in a semi-major axis of $a = 15.8 \mathrm{AU}$, an eccentricity of $e = 0.93$, and a minimum mass of the secondary of $m \sin i = 0.265 M_\odot$. Additional short-period RV variations closely resemble the signal of a Jupiter-mass planet orbiting the evolved primary component with a period of $291 \mathrm{d}$, but the period and amplitude of the putative orbit change strongly over time. Furthermore, in our stability analysis of the system, no stable orbits could be found in a large region around the best fit. Both of these findings deem a planetary cause of the RV variations unlikely. Most of the investigated alternative scenarios, such as an hierarchical triple or stellar spots, also fail to explain the observed variability convincingly. Due to its very eccentric binary orbit, it seems possible, however, that $\epsilon$ Cyg could be an extreme example of a heartbeat system.Comment: 17 pages, 13 figures, accepted to A&