Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering.

The timing of reproduction is an adaptive trait in many organisms. In plants, the timing, duration, and intensity of flowering differ between annual and perennial species. To identify interspecies variation in these traits, we studied introgression lines derived from hybridization of annual and perennial species, Arabis montbretiana and Arabis alpina, respectively. Recombination mapping identified two tandem A. montbretiana genes encoding MADS-domain transcription factors that confer extreme late flowering on A. alpina These genes are related to the MADS AFFECTING FLOWERING (MAF) cluster of floral repressors of other Brassicaceae species and were named A. montbretiana (Am) MAF-RELATED (MAR) genes. AmMAR1 but not AmMAR2 prevented floral induction at the shoot apex of A. alpina, strongly enhancing the effect of the MAF cluster, and MAR1 is absent from the genomes of all A. alpina accessions analyzed. Exposure of plants to cold (vernalization) represses AmMAR1 transcription and overcomes its inhibition of flowering. Assembly of the tandem arrays of MAR and MAF genes of six A. alpina accessions and three related species using PacBio long-sequence reads demonstrated that the MARs arose within the Arabis genus by interchromosomal transposition of a MAF1-like gene followed by tandem duplication. Time-resolved comparative RNA-sequencing (RNA-seq) suggested that AmMAR1 may be retained in A. montbretiana to enhance the effect of the AmMAF cluster and extend the duration of vernalization required for flowering. Our results demonstrate that MAF genes transposed independently in different Brassicaceae lineages and suggest that they were retained to modulate adaptive flowering responses that differ even among closely related species.

An Optically Pumped Magnetometer Working in the Light-Shift Dispersed Mz Mode.

We present an optically pumped magnetometer working in a new operational mode-the light-shift dispersed Mz (LSD-Mz) mode. It is realized combining various features; (1) high power off-resonant optical pumping; (2) Mz configuration, where pumping light and magnetic field of interest are oriented parallel to each other; (3) use of small alkali metal vapor cells of identical properties in integrated array structures, where two such cells are pumped by circularly polarized light of opposite helicity; and (4) subtraction of the Mz signals of these two cells. The LSD-Mz magnetometer's performance depends on the inherent and very complex interplay of input parameters. In order to find the configuration of optimal magnetometer resolution, a sensitivity analysis of the input parameters by means of Latin Hypercube Sampling was carried out. The resulting datasets of the multi-dimensional parameter space exploration were assessed by a subsequent physically reasonable interpretation. Finally, the best shot-noise limited magnetic field resolution was determined within that parameter space. As the result, using two 50 mm3 integrated vapor cells a magnetic field resolution below 10 fT/√Hz at Earth's magnetic field strength is possible.

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data.

Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.

The evolutionary root of flowering plants.

Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse taxon sampling among basal angiosperms. Here, we provide further evidence for concern over substitution model misspecification in analyses of chloroplast DNA sequences. We show that support for Amborella as the sole representative of the most basal angiosperm lineage is founded on sequence site patterns poorly described by time-reversible substitution models. Improving the fit between sequence data and substitution model identifies Trithuria, Nymphaeaceae, and Amborella as surviving relatives of the most basal lineage of flowering plants. This finding indicates that aquatic and herbaceous species dominate the earliest extant lineage of flowering plants. [; ; ; ; ; .].

Characteristics and performance of an intensity-modulated optically pumped magnetometer in comparison to the classical M(x) magnetometer.

We compare the performance of two methods for the synchronization of the atomic spins in optically pumped magnetometers: intensity modulation of the pump light and the classical M(x) method using B(1) field modulation. Both techniques use the same set-up and measure the resulting features of the light after passing a micro-fabricated Cs cell. The intensity-modulated pumping shows several advantages: better noise-limited magnetic field sensitivity, misalignment between pumping and spin synchronization is excluded, and magnetometer arrays without any cross-talk can be easily set up.

Light-shift suppression in a miniaturized Mx optically pumped Cs magnetometer array with enhanced resonance signal using off-resonant laser pumping.

The performance of an optically pumped Mx magnetometer with miniaturized Cs cell at earth's magnetic field strength (50 µT) is investigated. Operation using detuned high intensity laser light is shown to be superior to the conventional resonant operation in terms of the projected shot-noise-limited ( 50 fT/√Hz) and the actual noise-limited sensitivity using a noise compensation method. The Zeeman light shift effect, emerging due to the off-resonant circularly polarized laser radiation and leading to a strong orientational dependence of the measurement, is suppressed by averaging two identical magnetometer configurations pumped with oppositely circularly polarized light. A residual heading error within the range of 14 nT, limited by the present experimental characterization setup, was achieved.