Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species

Citation: Qiu, F., & Ungerer, M. C. (2018). Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species. BMC Plant Biology, 18(1). https://doi.org/10.1186/s12870-017-1223-zBackground: Long terminal repeat (LTR) retrotransposons are highly abundant in plant genomes and require transcriptional activity for their proliferative mode of replication. These sequences exist in plant genomes as diverse sublineages within the main element superfamilies (i.e., gypsy and copia). While transcriptional activity of these elements is increasingly recognized as a regular attribute of plant transcriptomes, it is currently unknown the extent to which different sublineages of these elements are transcriptionally active both within and across species. In the current report, we utilize next generation sequencing methods to examine genomic copy number abundance of diverse LTR retrotransposon sublineages and their corresponding levels of transcriptional activity in three diploid wild sunflower species, Helianthus agrestis, H. carnosus and H. porteri. Results: The diploid sunflower species under investigation differ in genome size 2.75-fold, with 2C values of 22.93 for H. agrestis, 12.31 for H. carnosus and 8.33 for H. porteri. The same diverse gypsy and copia sublineages of LTR retrotransposons were identified across species, but with gypsy sequences consistently more abundant than copia and with global gypsy sequence abundance positively correlated with nuclear genome size. Transcriptional activity was detected for multiple copia and gypsy sequences, with significantly higher activity levels detected for copia versus gypsy. Interestingly, of 11 elements identified as transcriptionally active, 5 exhibited detectable expression in all three species and 3 exhibited detectable expression in two species. Conclusions: Combined analyses of LTR retrotransposon genomic abundance and transcriptional activity across three sunflower species provides novel insights into genome size evolution and transposable element dynamics in this group. Despite considerable variation in nuclear genome size among species, relatively conserved patterns of LTR retrotransposon transcriptional activity were observed, with a highly overlapping set of copia and gypsy sequences observed to be transcriptionally active across species. A higher proportion of copia versus gypsy elements were found to be transcriptionally active and these sequences also were expressed at higher levels

Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

Citation: Tetreault, H. M., & Ungerer, M. C. (2016). Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. G3-Genes Genomes Genetics, 6(8), 2299-2308. doi:10.1534/g3.116.029082/-/DC1The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny

Ecological Genomics: Understanding Gene and Genome Function in the Natural Environment

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic variation. Likewise, genomic approaches are beginning to offer new insights into higher-level biological phenomena that previously occupied the realm of ecological investigation only. We discuss various approaches that are likely to be useful in ecological genomic studies and offer thoughts on where this field is headed in the future

A community of clones: Snow algae are diverse communities of spatially structured clones

Citation: Brown, S. P., Ungerer, M. C., & Jumpponen, A. (2016). A community of clones: Snow algae are diverse communities of spatially structured clones. International Journal of Plant Sciences, 177(5), 432-439. doi:10.1086/686019Premise of research. Snow algae are cosmopolitan and often colonize late-season snowpacks. These snow algae do not occur in isolation; rather, visible algal blooms consist of multispecies communities. Although several of these common snow algae have been characterized taxonomically, their inter- and intraspecific diversity remains unknown. Further, the phylogeographic and biogeographic structuring of snow algal species is poorly understood. Methodology. Algal communities were censused by sequencing the variable internal transcribed spacer 2 locus using Illumina MiSeq. We further analyzed two of the most common and abundant algal operational taxonomic units (OTUs) for biogeographic haplotype diversity. Pivotal results. Our data show that the communities are diverse and taxonomically broad (orders: Chlamydomonadales [74% of OTUs], Microthamniales [20% OTUs], and Chlorellales [6% OTUs]). We demonstrate that the two most common species (best nucleotide basic local alignment search tool match to Coenochloris sp. and Chlamydomonas sp.) have distinct haplotype distributions locally and regionally. Each sampled algal colony was dominated by one and only one haplotype, with negligible intraspecific haplotype diversity. Conclusions. Our results suggest that snow algae are communities of clones within a discrete patch yet are heterogeneous across the landscape. Thus, these communities are likely structured via strong priority effects, intense kin competition, and dispersal limitations. © 2016 by The University of Chicago. All rights reserved

Chemical Chaperones Improve Protein Secretion and Rescue Mutant Factor VIII in Mice with Hemophilia A.

nefficient intracellular protein trafficking is a critical issue in the pathogenesis of a variety of diseases and in recombinant protein production. Here we investigated the trafficking of factor VIII (FVIII), which is affected in the coagulation disorder hemophilia A. We hypothesized that chemical chaperones may be useful to enhance folding and processing of FVIII in recombinant protein production, and as a therapeutic approach in patients with impaired FVIII secretion. A tagged B-domain-deleted version of human FVIII was expressed in cultured Chinese Hamster Ovary cells to mimic the industrial production of this important protein. Of several chemical chaperones tested, the addition of betaine resulted in increased secretion of FVIII, by increasing solubility of intracellular FVIII aggregates and improving transport from endoplasmic reticulum to Golgi. Similar results were obtained in experiments monitoring recombinant full-length FVIII. Oral betaine administration also increased FVIII and factor IX (FIX) plasma levels in FVIII or FIX knockout mice following gene transfer. Moreover, in vitro and in vivo applications of betaine were also able to rescue a trafficking-defective FVIII mutant (FVIIIQ305P). We conclude that chemical chaperones such as betaine might represent a useful treatment concept for hemophilia and other diseases caused by deficient intracellular protein trafficking

Performance of high impedance resonators in dirty dielectric environments

High-impedance resonators are a promising contender for realizing long-distance entangling gates between spin qubits. Often, the fabrication of spin qubits relies on the use of gate dielectrics which are detrimental to the quality of the resonator. Here, we investigate loss mechanisms of high-impedance NbTiN resonators in the vicinity of thermally grown SiO2 and Al2O3 fabricated by atomic layer deposition. We benchmark the resonator performance in elevated magnetic fields and at elevated temperatures and find that the internal quality factors are limited by the coupling between the resonator and two-level systems of the employed oxides. Nonetheless, the internal quality factors of high-impedance resonators exceed 103 in all investigated oxide configurations which implies that the dielectric configuration would not limit the performance of resonators integrated in a spin-qubit device. Because these oxides are commonly used for spin qubit device fabrication, our results allow for straightforward integration of high-impedance resonators into spin-based quantum processors. Hence, these experiments pave the way for large-scale, spin-based quantum computers

Observational Constraints on Interstellar Grain Alignment

We present new multicolor photo-polarimetry of stars behind the Southern Coalsack. Analyzed together with multiband polarization data from the literature, probing the Chamaeleon I, Musca, rho Opiuchus, R CrA and Taurus clouds, we show that the wavelength of maximum polarization (lambda_max) is linearly correlated with the radiation environment of the grains. Using Far-Infrared emission data, we show that the large scatter seen in previous studies of lambda_max as a function of A_V is primarily due to line of sight effects causing some A_V measurements to not be a good tracer of the extinction (radiation field strength) seen by the grains being probed. The derived slopes in lambda_max vs. A_V, for the individual clouds, are consistent with a common value, while the zero intercepts scale with the average values of the ratios of total-to-selective extinction (R_V) for the individual clouds. Within each cloud we do not find direct correlations between lambda_max and R_V. The positive slope in consistent with recent developments in theory and indicating alignment driven by the radiation field. The present data cannot conclusively differentiate between direct radiative torques and alignment driven by H_2 formation. However, the small values of lambda_max(A_V=0), seen in several clouds, suggest a role for the latter, at least at the cloud surfaces. The scatter in the lambda_max vs. A_V relation is found to be associated with the characteristics of the embedded Young Stellar Objects (YSO) in the clouds. We propose that this is partially due to locally increased plasma damping of the grain rotation caused by X-rays from the YSOs.Comment: Accepted for publication in the Astrophysical Journa

Photon-mediated long range coupling of two Andreev level qubits

In a superconducting weak link, the supercurrent is carried by Andreev bound states (ABSs) formed by the phase-coherent reflection of electrons and their time-reversed partners. A single, highly transmissive ABS can serve as an ideal, compact two-level system, due to a potentially large energy difference to the next ABS. While the coherent manipulation of such Andreev levels qubits (ALQs) has been demonstrated, a long-range coupling between two ALQs, necessary for advanced qubit architectures, has not been achieved, yet. Here, we demonstrate a coherent remote coupling between two ALQs, mediated by a microwave photon in a novel superconducting microwave cavity coupler. The latter hosts two modes with different coupling rates to an external port. This allows us to perform fast readout of each qubit using the strongly coupled mode, while the weakly coupled mode is utilized to mediate the coupling between the qubits. When both qubits are tuned into resonance with the latter mode, we find excitation spectra with avoided-crossings, in very good agreement with the Tavis-Cummings model. Based on this model, we identify highly entangled two-qubit states for which the entanglement is mediated over a distance of six millimeters. This work establishes ALQs as compact and scalable solid-state qubits.Comment: 13 pages, 7 figure

Diversity of Flowering Responses in Wild Arabidopsis thaliana Strains

Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering under long days. Much of the difference in vernalization response is apparently due to variation at two epistatically acting loci, FRI and FLC. We present the response of over 150 wild accessions to three different environmental variables. In long days, FLC is among those genes whose expression is most highly correlated with flowering. In short days, FRI and FLC are less important, although their contribution is still significant. In addition, there is considerable variation not only in vernalization response, but also in the response to differences in day length or ambient growth temperature. The identification of accessions that flower relatively early or late in specific environments suggests that many of the flowering-time pathways identified by mutagenesis, such as those that respond to day length, contribute to flowering-time variation in the wild. In contrast to differences in vernalization requirement, which are mainly mediated by FRI and FLC, it seems that variation in these other pathways is due to allelic effects at several different loci

In-situ Tuning of the Electric Dipole Strength of a Double Dot Charge Qubit: Charge Noise Protection and Ultra Strong Coupling

Semiconductor quantum dots, where electrons or holes are isolated via electrostatic potentials generated by surface gates, are promising building blocks for semiconductor-based quantum technology. Here, we investigate double quantum dot (DQD) charge qubits in GaAs, capacitively coupled to high-impedance SQUID array and Josephson junction array resonators. We tune the strength of the electric dipole interaction between the qubit and the resonator in-situ using surface gates. We characterize the qubit-resonator coupling strength, qubit decoherence, and detuning noise affecting the charge qubit for different electrostatic DQD configurations. We find that all quantities can be tuned systematically over more than one order of magnitude, resulting in reproducible decoherence rates $\Gamma_2/2\pi<~5$ MHz in the limit of high interdot capacitance. Conversely, by reducing the interdot capacitance, we can increase the DQD electric dipole strength, and therefore its coupling to the resonator. By employing a Josephson junction array resonator with an impedance of $\sim4$ k$\Omega$ and a resonance frequency of $\omega_r/2\pi \sim 5.6$ GHz, we observe a coupling strength of $g/2\pi \sim 630$ MHz, demonstrating the possibility to achieve the ultrastrong coupling regime (USC) for electrons hosted in a semiconductor DQD. These results are essential for further increasing the coherence of quantum dot based qubits and investigating USC physics in semiconducting QDs.Comment: 24 pages, 13 figure