A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding.

The assembly and scaffolding of plant crop genomes facilitate the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato (Solanum lycopersicum) has been improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of tobacco mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT Nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV-resistant tomato variety. We show specific examples of how HiFi and ONT datasets can complement one another to improve assembly contiguity. We merged the HiFi and ONT assemblies to generate a long-read-only assembly where all 12 chromosomes were represented as 12 contiguous sequences (N50 = 68.5 Mbp). This chromosome scale assembly did not require scaffolding using an orthogonal data type. The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato genome assemblies that made use of genetic maps and Hi-C for scaffolding. Our long-read-only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1-Mbp region of the S. peruvianum genome during tomato breeding. Through marker studies and ONT-based comprehensive haplotyping we show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near-complete genome sequences.

ZmASY1 interacts with ZmPRD3 and is crucial for meiotic double-strand break formation in maize.

During meiosis, recombination-mediated pairing and synapsis of homologous chromosomes begin with programmed DNA double-strand breaks (DSBs). In yeast and mice, DSBs form in a tethered loop-axis complex, in which DSB sites are located within chromatin loops and tethered to the proteinaceous axial element (AE) by DSB-forming factors. In plants, the molecular connection between DSB sites and chromosome axes is poorly understood. By integrating genetic analysis, immunostaining technology, and protein-protein interaction studies, the putative factors linking DSB formation to chromosome axis were explored in maize meiosis. Here, we report that the AE protein ZmASY1 directly interacts with the DSB-forming protein ZmPRD3 in maize (Zea mays) and mediates DSB formation, synaptonemal complex assembly, and homologous recombination. ZmPRD3 also interacts with ZmPRD1, which plays a central role in organizing the DSB-forming complex. These results suggest that ZmASY1 and ZmPRD3 may work as a key module linking DSB sites to chromosome axes during DSB formation in maize. This mechanism is similar to that described in yeast and recently Arabidopsis involving the homologs Mer2/ZmPRD3 and HOP1/ZmASY1, thus indicating that the process of tethering DSBs in chromatin loops to the chromosome axes may be evolutionarily conserved in diverse taxa.

ZmPRD1 is essential for double-strand break formation, but is not required for bipolar spindle assembly during maize meiosis.

Homologs of PUTATIVE RECOMBINATION INITIATION DEFECT 1 (PRD1) are known to be essential for meiotic double-strand break (DSB) formation in mouse (Mus musculus), Arabidopsis, and rice (Oryza sativa). Recent research has shown that rice PRD1 also plays an unanticipated role in meiotic bipolar spindle assembly, revealing that PRD1 has multiple functions in plant meiosis. In this study, we characterize the meiotic function of PRD1 in maize (Zea mays; ZmPRD1). Our results show that Zmprd1 mutant plants display normal vegetative growth but have complete male and female sterility. Meiotic DSB formation is fully abolished in mutant meiocytes, leading to failure in homologous pairing, synapsis, and recombination. ZmPRD1 exhibits a different pattern of chromosome localization compared to its rice homologs. The ZmPRD1 protein interacts with several DSB-forming proteins, but does not directly interact with the kinetochore proteins REC8 and SGO1. Possibly as a result of this, there are no significant abnormalities of bipolar spindle assembly in Zmprd1 meiocytes. Overall, our results demonstrate that ZmPRD1 is essential for DSB formation and homologous recombination in maize meiosis. However, the recently-identified function of PRD1 in bipolar spindle assembly during rice meiosis is not conserved in maize.

Meiosis in crops: from genes to genomes.

Meiosis is a key feature of sexual reproduction. During meiosis homologous chromosomes replicate, recombine, and randomly segregate, followed by the segregation of sister chromatids to produce haploid cells. The unique genotypes of recombinant gametes are an essential substrate for the selection of superior genotypes in natural populations and in plant breeding. In this review we summarize current knowledge on meiosis in diverse monocot and dicot crop species and provide a comprehensive resource of cloned meiotic mutants in six crop species (rice, maize, wheat, barley, tomato, and Brassica species). Generally, the functional roles of meiotic proteins are conserved between plant species, but we highlight notable differences in mutant phenotypes. The physical lengths of plant chromosomes vary greatly; for instance, wheat chromosomes are roughly one order of magnitude longer than those of rice. We explore how chromosomal distribution for crossover recombination can vary between species. We conclude that research on meiosis in crops will continue to complement that in Arabidopsis, and alongside possible applications in plant breeding will facilitate a better understanding of how the different stages of meiosis are controlled in plant species.

Advances Towards How Meiotic Recombination Is Initiated: A Comparative View and Perspectives for Plant Meiosis Research.

Meiosis is an essential cell-division process for ensuring genetic diversity across generations. Meiotic recombination ensures the accuracy of genetic interchange between homolous chromosomes and segregation of parental alleles. Programmed DNA double-strand breaks (DSBs), catalyzed by the evolutionarily conserved topoisomerase VIA (a subunit of the archaeal type II DNA topoisomerase)-like enzyme Spo11 and several other factors, is a distinctive feature of meiotic recombination initiation. The meiotic DSB formation and its regulatory mechanisms are similar among species, but certain aspects are distinct. In this review, we introduced the cumulative knowledge of the plant proteins crucial for meiotic DSB formation and technical advances in DSB detection. We also summarized the genome-wide DSB hotspot profiles for different model organisms. Moreover, we highlighted the classical views and recent advances in our knowledge of the regulatory mechanisms that ensure the fidelity of DSB formation, such as multifaceted kinase-mediated phosphorylation and the consequent high-dimensional changes in chromosome structure. We provided an overview of recent findings concerning DSB formation, distribution and regulation, all of which will help us to determine whether meiotic DSB formation is evolutionarily conserved or varies between plants and other organisms.

ZmRAD51C is Essential for Double-Strand Break Repair and Homologous Recombination in Maize Meiosis.

Radiation sensitive 51 (RAD51) recombinases play crucial roles in meiotic double-strand break (DSB) repair mediated by homologous recombination (HR) to ensure the correct segregation of homologous chromosomes. In this study, we identified the meiotic functions of ZmRAD51C, the maize homolog of Arabidopsis and rice RAD51C. The Zmrad51c mutants exhibited regular vegetative growth but complete sterility for both male and female inflorescence. However, the mutants showed hypersensitivity to DNA damage by mitomycin C. Cytological analysis indicated that homologous chromosome pairing and synapsis were rigorously inhibited, and meiotic chromosomes were often entangled from diplotene to metaphase I, leading to chromosome fragmentation at anaphase I. Immunofluorescence analysis showed that although the signals of the axial element absence of first division (AFD1) and asynaptic1 (ASY1) were normal, the assembly of the central element zipper1 (ZYP1) was severely disrupted. The DSB formation was normal in Zmrad51c meiocytes, symbolized by the regular occurrence of γH2AX signals. However, RAD51 and disrupted meiotic cDNA 1 (DMC1) signals were never detected at the early stage of prophase I in the mutant. Taken together, our results indicate that ZmRAD51C functions crucially for both meiotic DSB repair and homologous recombination in maize.

Experimental demonstration of hybrid improper ferroelectricity and the presence of abundant charged walls in (Ca,Sr)3Ti2O7 crystals.

On the basis of successful first-principles predictions of new functional ferroelectric materials, a number of new ferroelectrics have been experimentally discovered. Using trilinear coupling of two types of octahedron rotation, hybrid improper ferroelectricity has been theoretically predicted in ordered perovskites and the Ruddlesden-Popper compounds (Ca3Ti2O7, Ca3Mn2O7 and (Ca/Sr/Ba)3(Sn/Zr/Ge)2O7). However, the ferroelectricity of these compounds has never been experimentally confirmed and even their polar nature has been under debate. Here we provide the first experimental demonstration of room-temperature switchable polarization in bulk crystals of Ca3Ti2O7, as well as Sr-doped Ca3Ti2O7. Furthermore, (Ca, Sr)3Ti2O7 is found to exhibit an intriguing ferroelectric domain structure resulting from orthorhombic twins and (switchable) planar polarization. The planar domain structure accompanies abundant charged domain walls with conducting head-to-head and insulating tail-to-tail configurations, which exhibit a conduction difference of two orders of magnitude. These discoveries provide new research opportunities, not only for new stable ferroelectrics of Ruddlesden-Popper compounds, but also for meandering conducting domain walls formed by planar polarization.

Toward the Intrinsic Limit of the Topological Insulator Bi_{2}Se_{3}.

Combining high resolution scanning tunneling microscopy and first principles calculations, we identified the major native defects, in particular the Se vacancies and Se interstitial defects, that are responsible for the bulk conduction and nanoscale potential fluctuations in single crystals of archetypal topological insulator Bi_{2}Se_{3}. Here it is established that the defect concentrations in Bi_{2}Se_{3} are far above the thermodynamic limit, and that the growth kinetics dominate the observed defect concentrations. Furthermore, through careful control of the synthesis, our tunneling spectroscopy suggests that our best samples are approaching the intrinsic limit with the Fermi level inside the band gap without introducing extrinsic dopants.

Harnessing clonal gametes in hybrid crops to engineer polyploid genomes.

Heterosis boosts crop yield; however, harnessing additional progressive heterosis in polyploids is challenging for breeders. We bioengineered a 'mitosis instead of meiosis' (MiMe) system that generates unreduced, clonal gametes in three hybrid tomato genotypes and used it to establish polyploid genome design. Through the hybridization of MiMe hybrids, we generated '4-haplotype' plants that encompassed the complete genetics of their four inbred grandparents, providing a blueprint for exploiting polyploidy in crops.

Apomixis.

Wang and Underwood introduce apomixis in plants.

Narrowband organic photodetectors - towards miniaturized, spectroscopic sensing.

Omnipresent quality monitoring in food products, blood-oxygen measurement in lightweight conformal wrist bands, or data-driven automated industrial production: Innovation in many fields is being empowered by sensor technology. Specifically, organic photodetectors (OPDs) promise great advances due to their beneficial properties and low-cost production. Recent research has led to rapid improvement in all performance parameters of OPDs, which are now on-par or better than their inorganic counterparts, such as silicon or indium gallium arsenide photodetectors, in several aspects. In particular, it is possible to directly design OPDs for specific wavelengths. This makes expensive and bulky optical filters obsolete and allows for miniature detector devices. In this review, recent progress of such narrowband OPDs is systematically summarized covering all aspects from narrow-photo-absorbing materials to device architecture engineering. The recent challenges for narrowband OPDs, like achieving high responsivity, low dark current, high response speed, and good dynamic range are carefully addressed. Finally, application demonstrations covering broadband and narrowband OPDs are discussed. Importantly, several exciting research perspectives, which will stimulate further research on organic-semiconductor-based photodetectors, are pointed out at the very end of this review.

Ultrasound far-focused pixel-based imaging using Wiener postfilter scaled by adjustable zero-cross factor.

Synthetic aperture (SA) imaging can provide a uniform lateral resolution but an insufficient signal-to-noise ratio (SNR). SA method with bidirectional pixel-based focusing (SA-BiPBF) has the ability to obtain a higher quality image than conventional SA imaging. In this paper, an enhanced SA-BiPBF named full aperture received far-focused pixel-based (FrFPB) is firstly proposed to obtain a high resolution image. An adjustable zero-cross factor scaled Wiener postfilter (AZFsW) is then implemented in FrFPB for improving contrast ratio (CR). The adjustable zero-cross factor is calculated using the polarity of echo signals sequence with an adjustable coefficient σ to estimate the signal coherence, and it is combined with Wiener postfilter to obtain a good capability of noise reduction and background speckle pattern preservation. Simulation and experiments have been conducted to evaluate the imaging performance of the proposed methods. Results show that FrFPB can obviously improve the resolution in comparison with SA-BiPBF, and contrast-to-noise ratio (CNR) and speckle signal-to-noise ratio (sSNR) are retained. In addition, AZFsW can achieve a much higher CR than SA-BiPBF. When σ is 0.6, the CR improvement is 96.7% in simulation, 78.7% in phantom experiment, and 49.2% in in-vivo experiment. To evaluate the imaging performance of AZFsW, coherence factor, conventional Wiener postfilter, and scaled Wiener postfilter are implemented. The imaging results show that when σ is in the range of [0.6, 0.7], AZFsW exhibits a satisfying comprehensive imaging performance.

Optical Distance Measurement Based on Induced Nonlinear Photoresponse of High-Performance Organic Near-Infrared Photodetectors.

Extraction barriers are usually undesired in organic semiconductor devices since they lead to reduced device performance. In this work, we intentionally introduce an extraction barrier for holes, leading to nonlinear photoresponse. The effect is utilized in near-infrared (NIR) organic photodetectors (OPDs) to perform distance measurements, as delineated in the focus-induced photoresponse technique (FIP). The extraction barrier is introduced by inserting an anodic interlayer with deeper highest occupied molecular orbital (HOMO), compared to the donor material, into a well-performing OPD. With increasing irradiance, achieved by decreasing the illumination spot area on the OPD, a higher number of holes pile up at the anode, counteracting the built-in field and increasing charge-carrier recombination in the bulk. This intended nonlinear response of the photocurrent to the irradiance allows determining the distance between the OPD and the light source. We demonstrate fully vacuum-deposited organic NIR optical distance photodetectors with a detection area up to 256 mm2 and detection wavelengths at 850 and 1060 nm. Such NIR OPDs have a high potential for precise, robust, low-cost, and simple optical distance measurement setups.

Miniaturized VIS-NIR Spectrometers Based on Narrowband and Tunable Transmission Cavity Organic Photodetectors with Ultrahigh Specific Detectivity above 1014 Jones.

Spectroscopic photodetection plays a key role in many emerging applications such as context-aware optical sensing, wearable biometric monitoring, and biomedical imaging. Photodetectors based on organic semiconductors open many new possibilities in this field. However, ease of processing, tailorable optoelectronic properties, and sensitivity for faint light are still significant challenges. Here, the authors report a novel concept for a tunable spectral detector by combining an innovative transmission cavity structure with organic absorbers to yield narrowband organic photodetection in the wavelength range of 400-1100 nm, fabricated in a full-vacuum process. Benefiting from this strategy, one of the best performed narrowband organic photodetectors is achieved with a finely wavelength-selective photoresponse (full-width-at-half-maximum of ≈40 nm), ultrahigh specific detectivity above 1014 Jones, the maximum response speed of 555 kHz, and a large dynamic range up to 168 dB. Particularly, an array of transmission cavity organic photodetectors is monolithically integrated on a small substrate to showcase a miniaturized spectrometer application, and a true proof-of-concept transmission spectrum measurement is successfully demonstrated. The excellent performance, the simple device fabrication as well as the possibility of high integration of this new concept challenge state-of-the-art low-noise silicon photodetectors and will mature the spectroscopic photodetection into technological realities.

ZmCom1 Is Required for Both Mitotic and Meiotic Recombination in Maize.

CtIP/Ctp1/Sae2/Com1, a highly conserved protein from yeast to higher eukaryotes, is required for DNA double-strand break repair through homologous recombination (HR). In this study, we identified and characterized the COM1 homolog in maize. The ZmCom1 gene is abundantly expressed in reproductive tissues at meiosis stages. In ZmCom1-deficient plants, meiotic chromosomes are constantly entangled as a formation of multivalents and accompanied with chromosome fragmentation at anaphase I. In addition, the formation of telomere bouquet, homologous pairing and synapsis were disturbed. The immunostaining assay showed that the localization of ASY1 and DSY2 was normal, while ZYP1 signals were severely disrupted in Zmcom1 meiocytes, indicating that ZmCom1 is critically required for the proper SC assembly. Moreover, RAD51 signals were almost completely absent in Zmcom1 meiocytes, implying that COM1 is required for RAD51 loading. Surprisingly, in contrast to the Atcom1 and Oscom1 mutants, Zmcom1 mutant plants exhibited a number of vegetative phenotypes under normal growth condition, which may be partly attributed to mitotic aberrations including chromosomal fragmentation and anaphase bridges. Taken together, our results suggest that although the roles of COM1 in HR process seem to be primarily conserved, the COM1 dysfunction can result in the marked dissimilarity in mitotic and meiotic outcomes in maize compared to Arabidopsis and rice. We suggest that this character may be related to the discrete genome context.

The First Room-Temperature Ferroelectric Sn Insulator and Its Polarization Switching Kinetics.

Sr3 Sn2 O7 is the first room-temperature ferroelectric Sn insulator with switchable electric polarization. The ferroelastic twin domains are observed using a polarized optical microscope. The polarization hysteresis loop clearly demonstrates the ferroelectric property. Intriguing polarization switching kinetics are observed through an in situ poling process using a dark-field transmission electron microscopy technique.

Unveiling hidden ferrimagnetism and giant magnetoelectricity in polar magnet Fe2Mo3O8.

Magnetoelectric (ME) effect is recognized for its utility for low-power electronic devices. Largest ME coefficients are often associated with phase transitions in which ferroelectricity is induced by magnetic order. Unfortunately, in these systems, large ME response is revealed only upon elaborate poling procedures. These procedures may become unnecessary in single-polar-domain crystals of polar magnets. Here we report giant ME effects in a polar magnet Fe2Mo3O8 at temperatures as high as 60 K. Polarization jumps of 0.3 µC/cm(2), and repeated mutual control of ferroelectric and magnetic moments with differential ME coefficients on the order of 10(4) ps/m are achieved. Importantly, no electric or magnetic poling is needed, as necessary for applications. The sign of the ME coefficients can be switched by changing the applied "bias" magnetic field. The observed effects are associated with a hidden ferrimagnetic order unveiled by application of a magnetic field.