A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification.

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

Flexible rotation of linear polarization conversion with a frequency selective surface.

A high-efficiency transmitted polarization converter based on a frequency selective surface (FSS) is proposed in this paper. The FSS-based polarization converter (FSS-PC) is designed based on receiving-via-transmitting (RVT) structure. The receiving and transmitting antenna structures are interconnected by the transmission line, designed in the form of metallized via holes. For any linearly polarized (LP) electromagnetic wave, our proposed FSS-PC has the capability to convert it into another LP electromagnetic wave. This converted wave will have a counterclockwise rotation angle of 2φ relative to the incident wave at 11 GHz. This is achieved by adjusting the relative azimuth φ between the polarization plane of the incident LP wave's electric field and the converter. Meanwhile, the FSS-PC can achieve exceptionally high polarization conversion above -0.30 dB at the central frequency of 11 GHz. Furthermore, as the azimuth of the incident electric field varies, this high-efficiency polarization conversion capability remains stable. The prototype has been fabricated and measured, and the measured results agree well with the simulated ones, thus confirming the effectiveness of the proposed design.

Design of a Reconfigurable Ultra-Wideband Terahertz Polarization Rotator Based on Graphene Metamaterial.

In this work, a reconfigurable ultra-wideband transmissive terahertz polarization rotator based on graphene metamaterial is proposed that can switch between two states of polarization rotation within a broad terahertz band by changing the Fermi level of graphene. The proposed reconfigurable polarization rotator is based on a two-dimensional periodic array of multilayer graphene metamaterial structure, which is composed of metal grating, graphene grating, silicon dioxide thin film, and a dielectric substrate. The graphene metamaterial can achieve high co-polarized transmission of a linearly polarized incident wave at the off-state of the graphene grating without applying the bias voltage. Once the specially designed bias voltage is applied to change the Fermi level of graphene, the polarization rotation angle of linearly polarized waves is switched to 45° by the graphene metamaterial at the on-state. The working frequency band with 45-degree linear polarized transmission remaining above 0.7 and the polarization conversion ratio (PCR) above 90% is from 0.35 to 1.75 THz, and the relative bandwidth reaches 133.3% of the central working frequency. Furthermore, even with oblique incidence at large angles, the proposed device retains high-efficiency conversion in a broad band. The proposed graphene metamaterial offers a novel approach for the design of a terahertz tunable polarization rotator and is expected to be applied in the applications of terahertz wireless communication, imaging, and sensing.

Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification.

BACKGROUND: Brassica oleracea includes several morphologically diverse, economically important vegetable crops, such as the cauliflower and cabbage. However, genetic variants, especially large structural variants (SVs), that underlie the extreme morphological diversity of B. oleracea remain largely unexplored. RESULTS: Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~ 120 K high-confidence SVs. Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development. CONCLUSIONS: This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding.

Genome Sequence of Fusarium oxysporum f. sp. conglutinans, the Etiological Agent of Cabbage Fusarium Wilt.

Fusarium oxysporum f. sp. conglutinans is the causal agent of Fusarium wilt of cabbage (Brassica oleracea var. capitata L.), which results in severe yield loss. Here, we report a high-quality genome sequence of a race 1 strain (IVC-1) of F. oxysporum f. sp. conglutinans, which was assembled using a combination of PacBio long-read and Illumina short-read sequences. The assembled IVC-1 genome has a total size of 71.18 Mb, with a contig N50 length of 4.59 Mb, and encodes 23,374 predicted protein-coding genes. The high-quality genome of IVC-1 provides a valuable resource for facilitating our understanding of F. oxysporum f. sp. conglutinans-cabbage interaction.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome-Wide Analysis of Basic Helix-Loop-Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.).

Basic helix-loop-helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

Genome-wide identification of genes encoding putative secreted E3 ubiquitin ligases and functional characterization of PbRING1 in the biotrophic protist Plasmodiophora brassicae.

The E3 ubiquitin ligases are key regulators of protein ubiquitination, which have been shown to be involved in a variety of cellular responses to both biotic and abiotic stresses in eukaryotes. However, the E3 ubiquitin ligase homologues in the soil-borne plant pathogen Plasmodiophora brassicae, the causal agent of clubroot disease of crucifer crops worldwide, remain largely unknown. In this study, we characterized secreted E3 ubiquitin ligases, a group of proteins known to be involved in virulence in many pathogens, in a plasmodiophorid P. brassicae. Genome-wide search in the P. brassicae genome retrieved 139 putative E3 ubiquitin ligases, comprising of 115 RING, 15 HECT, 1 HECT-like, and 8 U-box E3 ubiquitin ligases. Among these E3 ubiquitin ligases, 11 RING, 1 U-box, and 3 HECT were found to harbor signal peptide. Based on published RNA-seq data (Schwelm et al. in Sci Rep 5:11153, 2015), we found that these genes were differentially expressed in distinct life stages including germinating spores, maturing spores, and plasmodia. We characterized one potential secreted E3 ubiquitin ligase, PbRING1 (PBRA_000499). Yeast invertase assay showed that PbRING1 harbors a functional N-terminal signal peptide. PbRING1 also harbors a really interested new gene (RING) domain at its C terminus, which was found to display the E3 ligase activity in vitro. Collectively, this study provides a comprehensive insight into the reservoir of putative secreted E3 ligases in P. brassicae.

Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses.

BACKGROUND: The SWEET proteins are a group of sugar transporters that play a role in sugar efflux during a range of biological processes, including stress responses. However, there has been no comprehensive analysis of the SWEET family genes in Brassica oleracea (BoSWEET), and the evolutionary pattern, phylogenetic relationship, gene characteristics of BoSWEET genes and their expression patterns under biotic and abiotic stresses remain largely unexplored. RESULTS: A total of 30 BoSWEET genes were identified and divided into four clades in B. oleracea. Phylogenetic analysis of the BoSWEET proteins indicated that clade II formed first, followed by clade I, clade IV and clade III, successively. Clade III, the newest clade, shows signs of rapid expansion. The Ks values of the orthologous SWEET gene pairs between B. oleracea and Arabidopsis thaliana ranged from 0.30 to 0.45, which estimated that B. oleracea diverged from A. thaliana approximately 10 to 15 million years ago. Prediction of transmembrane regions showed that eight BoSWEET proteins contain one characteristic MtN3_slv domain, twenty-one contain two, and one has four. Quantitative reverse transcription-PCR (qRT-PCR) analysis revealed that five BoSWEET genes from clades III and IV exhibited reduced expression levels under chilling stress. Additionally, the expression levels of six BoSWEET genes were up-regulated in roots of a clubroot-susceptible cabbage cultivar (CS-JF1) at 7 days after inoculation with Plasmodiophora brassicae compared with uninoculated plants, indicating that these genes may play important roles in transporting sugars into sink roots associated with P. brassicae colonization in CS-JF1. Subcellular localization analysis of a subset of BoSWEET proteins indicated that they are localized in the plasma membrane. CONCLUSIONS: This study provides important insights into the evolution of the SWEET gene family in B. oleracea and other species, and represents the first study to characterize phylogenetic relationship, gene structures and expression patterns of the BoSWEET genes. These findings provide new insights into the complex transcriptional regulation of BoSWEET genes, as well as potential candidate BoSWEET genes that promote sugar transport to enhance chilling tolerance and clubroot disease resistance in cabbage.

Genome-Wide Identification and Expression Profiling of Sugar Transporter Protein (STP) Family Genes in Cabbage (Brassica oleracea var. capitata L.) Reveals their Involvement in Clubroot Disease Responses.

Sugar transporter protein (STP) genes are involved in multiple biological processes, such as plant responses to various stresses. However, systematic analysis and functional information of STP family genes in Brassica oleracea are very limited. A comprehensive analysis was carried out to identify BoSTP genes and dissect their phylogenetic relationships and to investigate the expression profiles in different organs and in response to the clubroot disease. A total of 22 BoSTP genes were identified in the B. oleracea genome and they were further classified into four clades based on the phylogenetic analysis. All the BoSTP proteins harbored the conserved sugar transporter (Sugar_tr, PF00083) domain, and the majority of them contained 12 transmembrane helices (TMHs). Rates of synonymous substitution in B. oleracea relative to Arabidopsis thaliana indicated that STP genes of B. oleracea diverged from those of A. thaliana approximately 16.3 million years ago. Expression profiles of the BoSTP genes in different organs derived from RNA-Seq data indicated that a large number of the BoSTP genes were expressed in specific organs. Additionally, the expression of BoSTP4b and BoSTP12 genes were induced in roots of the clubroot-susceptible cabbage (CS-JF1) at 28 days after inoculation with Plasmodiophora brassicae, compared with mock-inoculated plants. We speculated that the two BoSTPs might be involved in monosaccharide unloading and carbon partitioning associated with P. brassicae colonization in CS-JF1. Subcellular localization analysis indicated that the two BoSTP proteins were localized in the cell membrane. This study provides insights into the evolution and potential functions of BoSTPs.

Ultra-broadband linear polarization converter based on anisotropic metasurface.

Through the manipulation of co-polarized reflection and cross-polarized reflection from a periodic array of metal-dielectric-metal resonators, a plethora of unprecedented metamaterial devices have been successfully demonstrated, such as perfect absorber and polarization converter. Recently, some broadband absorbers based on anisotropic resonators have been reported, which are actually poor absorbers when the cross-polarized reflection is considered. Here, we demonstrate that an ultra-wideband and high-efficiency reflective cross-polarization convertor can be achieved by breaking the symmetry of the resonator unit of a perfect absorber. Simulation results show that the polarization conversion ratio of the proposed metasurface is above 90% in the frequency range from 6.67 to 17.1 GHz and the relative bandwidth reaches 87.7%. The experimental results are in good agreement with the simulation results. The method paves a new way for the design of broadband polarization convertor, which can also be extended to the terahertz band.

Ultra-broadband wide-angle linear polarization converter based on H-shaped metasurface.

We report the design, fabrication, and measurement of an ultra-broadband wide-angle reflective cross-polarization convertor using the compact H-shaped metasurface. The significant bandwidth expansion is attributed to the four electromagnetic resonances generated in an H-shaped unit. The simulation results show that the polarization conversion ratio (PCR) of the proposed metasurface is above 90% in the frequency range from 7 to 19.5 GHz and the relative bandwidth reaches 94%. The proposed metasurface is valid for a wide range of incident angles, and the mean polarization conversion ratio remains 80% even though the incident angle reaches 41.5°. The experimental results are in good agreement with the simulation results. Compared with the previous designs, the proposed linear polarization converter has a simple geometry but an excellent performance and hence has potential applications in microwave communications, remote sensors, and imaging systems.

Dual-band transmission polarization converter based on planar-dipole pair frequency selective surface.

A novel linear polarization converter operating in C- and X-bands with high polarization conversion ratio is described and demonstrated based on frequency selective surface. The building element is a planar-dipole pair, which is orthogonally printed on a double-layer substrate and vertically connected by a pair of through-via holes functioning as a quasi-two-wire transmission line coupler. A perforated metal shielding layer is sandwiched between the double-layer structure to only support a transverse electric and magnetic (TEM) mode coupling between the top and bottom dipolar components. The front dipole responds to the incident transverse electric (TE) wave, and sends the induced current into the two-wire transmission line to feed the bottom dipole. The bottom dipole is orthogonal or oriented at an arbitrary angle with respect to the top one, and a resultant outgoing transverse magnetic (TM) wave or arbitrary orientation polarized wave can be achieved. In addition, a bidirectional orthogonal polarization converter is realized by using double orthogonally arranged planar-dipole pairs, which are also printed on the same double-layer substrate.

Genome-wide identification, phylogeny, evolution, and expression patterns of MtN3/saliva/SWEET genes and functional analysis of BcNS in Brassica rapa.

BACKGROUND: Members of the MtN3/saliva/SWEET gene family are present in various organisms and are highly conserved. Their precise biochemical functions remain unclear, especially in Chinese cabbage. Based on the whole genome sequence, this study aims to identify the MtN3/saliva/SWEETs family members in Chinese cabbage and to analyze their classification, gene structure, chromosome distribution, phylogenetic relationship, expression pattern, and biological functions. RESULTS: We identified 34 SWEET genes in Chinese cabbage and analyzed their localization on chromosomes and transmembrane regions of their corresponding proteins. Analysis of a phylogenetic tree indicated that there were at least 17 supposed ancestor genes before the separation in Brassica rapa and Arabidopsis. The expression patterns of these genes in different tissues and flower developmental stages of Chinese cabbage showed that they are mainly involved in reproductive development. The Ka/Ks ratio between paralogous SWEET gene pairs of B. rapa were far less than 1. In our previous study, At2g39060 homologous gene Bra000116 (BraSWEET9, also named BcNS, Brassica Nectary and Stamen) played an important role during flower development in Chinese cabbage. Instantaneous expression experiments in onion epidermal cells showed that the gene encoding this protein is localized to the plasma membrane. A basal nectary split is the phenotype of transgenic plants transformed with the antisense expression vector. CONCLUSION: This study is the first to perform a sequence analysis, structures analysis, physiological and biochemical characteristics analysis of the MtN3/saliva/SWEETs gene in Chinese cabbage and to verify the function of BcNS. A total of 34 SWEET genes were identified and they are distributed among ten chromosomes and one scaffold. The Ka/Ks ratio implies that the duplication genes suffered strong purifying selection for retention. These genes were differentially expressed in different floral organs. The phenotypes of the transgenic plants indicated that BcNs participates in the development of the floral nectary. This study provides a basis for further functional analysis of the MtN3/saliva/SWEETs gene family.

Tailoring electromagnetically induced transparency with different coupling mechanisms.

Tailoring electromagnetically induced transparency with two different coupling mechanisms has been numerically demonstrated. The results show that EIT based on simultaneous electric resonance and magnetic resonance has relatively larger coupling distance compared with that based on electric resonance near field coupling to magnetic resonance. The relatively large coupling distance is due to the relatively small susceptibility change. For EIT based on simultaneous electric resonance and magnetic resonance, not only incident electric field but also the incident magnetic field pays a role on the susceptibility of system. The influence of the incident magnetic field leads to relatively smaller susceptibility change compared with that based on electric resonance near field coupling to magnetic resonance.

Optimization for nonmagnetic concentrator with minimized scattering.

Based on the generalized transformation for a nonmagnetic cylindrical concentrator, we present nonlinear coordinate transformations to realize excellent concentrating performance with minimized scattering. By matching the impedance at both the inner and outer boundaries and utilizing nonlinear optimization techniques, the best parameters of the nonlinear transformation can be determined. Results show that the concentrating power is sensitive to the impedance at the inner interface. In addition, an alternating layered system consisting of nonmagnetic isotropic materials is applied to experimentally mimic the concentrator, and excellent concentrating performances have been observed.

Cylindrical optimized nonmagnetic concentrator with minimized scattering.

By using optimized transformation function, we research on a minimized scattering nonmagnetic concentrator, which can realize impedance matching at the inner and the outer boundaries. It has been demonstrated that the optimized transformation function method can improve the concentrating performance remarkably. The cylindrical anisotropic shell can be mimicked by radial symmetrical sectors which alternate in composition between two profiles of isotropic dielectrics, and the permittivity in each sector can be properly determined by the effective medium theory. The nonmagnetic concentrator has been validated by full-wave finite element simulations. We can believe that this work will improve the flexibilities for the EM concentrator design.

Controlling electromagnetic scattering of a cavity by transformation media.

Based on the transformation media theory, we proposed a way to control the scattering of a cavity, or trench, located on a metallic plane. Specifically, we show how is possible to design transformation medium to fill up a cavity with arbitrary cross section, which is capable of enhancing the specularly reflection wave. As the inverse problem, we also address the design of transformation medium coating, which is laid on the metallic plane, to mimic the scattering of the cavity. Based on the effective medium theory, the transformation medium for the case of a polygonal cavity can be realized by oblique layered structures, and each layered structure is consisting of two kinds of isotropic dielectrics, thus leading an ease of practical fabrication.