The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids.

Polyploidization is important to the evolution of plants. Subgenome dominance is a distinct phenomenon associated with most allopolyploids. A gene on the dominant subgenome tends to express to higher RNA levels in all organs as compared to the expression of its syntenic paralogue (homoeolog). The mechanism that underlies the formation of subgenome dominance remains unknown, but there is evidence for the involvement of transposon/DNA methylation density differences nearby the genes of parents as being causal. The subgenome with lower density of transposon and methylation near genes is positively associated with subgenome dominance. Here, we generated eight generations of allotetraploid progenies from the merging of parental genomes Brassica rapa and Brassica oleracea. We found that transposon/methylation density differ near genes between the parental (rapa:oleracea) existed in the wide hybrid, persisted in the neotetraploids (the synthetic Brassica napus), but these neotetraploids expressed no expected subgenome dominance. This absence of B. rapa vs. B. oleracea subgenome dominance is particularly significant because, while there is no negative relationship between transposon/methylation level and subgenome dominance in the neotetraploids, the more ancient parental subgenomes for all Brassica did show differences in transposon/methylation densities near genes and did express, in the same samples of cells, biased gene expression diagnostic of subgenome dominance. We conclude that subgenome differences in methylated transposon near genes are not sufficient to initiate the biased gene expressions defining subgenome dominance. Our result was unexpected, and we suggest a "nuclear chimera" model to explain our data.

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus.

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.

Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra.

Cultivated spinach (Spinacia oleracea) is a dioecious species. We report high-quality genome sequences for its two closest wild relatives, Spinacia turkestanica and Spinacia tetrandra, which are also dioecious, and are used to study the genetics of spinach domestication. Using a combination of genomic approaches, we assembled genomes of both these species and analyzed them in comparison with the previously assembled S. oleracea genome. These species diverged c. 6.3 million years ago (Ma), while cultivated spinach split from S. turkestanica 0.8 Ma. In all three species, all six chromosomes include very large gene-poor, repeat-rich regions, which, in S. oleracea, are pericentromeric regions with very low recombination rates in both male and female genetic maps. We describe population genomic evidence that the similar regions in the wild species also recombine rarely. We characterized 282 structural variants (SVs) that have been selected during domestication. These regions include genes associated with leaf margin type and flowering time. We also describe evidence that the downy mildew resistance loci of cultivated spinach are derived from introgression from both wild spinach species. Collectively, this study reveals the genome architecture of spinach assemblies and highlights the importance of SVs during the domestication of cultivated spinach.

Evolution of the spinach sex-linked region within a rarely recombining pericentromeric region.

Sex chromosomes have evolved independently in many different plant lineages. Here, we describe reference genomes for spinach (Spinacia oleracea) X and Y haplotypes by sequencing homozygous XX females and YY males. The long arm of 185-Mb chromosome 4 carries a 13-Mb X-linked region (XLR) and 24.1-Mb Y-linked region (YLR), of which 10 Mb is Y specific. We describe evidence that this reflects insertions of autosomal sequences creating a "Y duplication region" or "YDR" whose presence probably directly reduces genetic recombination in the immediately flanking regions, although both the X and Y sex-linked regions are within a large pericentromeric region of chromosome 4 that recombines rarely in meiosis of both sexes. Sequence divergence estimates using synonymous sites indicate that YDR genes started diverging from their likely autosomal progenitors about 3 MYA, around the time when the flanking YLR stopped recombining with the XLR. These flanking regions have a higher density of repetitive sequences in the YY than the XX assembly and include slightly more pseudogenes compared with the XLR, and the YLR has lost about 11% of the ancestral genes, suggesting some degeneration. Insertion of a male-determining factor would have caused Y linkage across the entire pericentromeric region, creating physically small, highly recombining, terminal pseudoautosomal regions. These findings provide a broader understanding of the origin of sex chromosomes in spinach.

Cervical lymph node metastasis as the first symptom of combined anaplastic thyroid carcinoma (squamous cell carcinoma) and follicular carcinoma: a case report.

BACKGROUND: Anaplastic thyroid carcinoma(ATC) is a rare pathological type of thyroid malignancy. Primary squamous cell carcinoma of thyroid(PSCCT) is now considered as a subtype of ATC, hereinafter referred to as ATC-SCC subtype. ATC-SCC subtype combined with follicular thyroid carcinoma is exceedingly rare, with fewer cases reported. The ATC-SCC subtype is a highly invasive tumor with a poor prognosis for patients after metastasis occurs, and current treatment of this type of tumor is tricky. CASE PRESENTATION: A 68-year-old female patient presented with a gradually growing swelling of right cervical region. Comprehensive auxiliary examinations and postoperative pathology confirmed the diagnosis of ATC-SCC subtype with follicular thyroid carcinoma, and the metastasis squamous cell carcinoma of the right cervical lymph nodes originates from ATC-SCC subtype. The patient received chemoradiotherapy postoperative. However, the residual cervical lymph nodes metastasis with squamous cell carcinoma still infiltrated surrounding structures in the neck extensively after palliative resection. The patient died 7 months after surgery. CONCLUSION: Our case highlights that cervical lymph node metastasis may be a significant factor in the poor prognosis of ATC-SCC subtype. This malignancy should be detected and treated early.

BRAD V3.0: an upgraded Brassicaceae database.

The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.

Effects of White Noise on Pain Scores and Salivary Cortisol Levels in Surgical Neonates: A Randomized Controlled Trial.

BACKGROUND: Neonates experience varying intensities of pain after surgery. While white noise has been used for postoperative pain relief in infants, its effects on neonates after surgery need further exploration. PURPOSE: This study aimed to evaluate the effects of white noise on pain scores and salivary cortisol levels in surgical neonates. METHODS: In this randomized controlled trial, 64 neonates scheduled for surgery were recruited and assigned by block randomization into 2 groups. The intervention group listened to white noise at 50 dB, while the control group listened to white noise at 0 dB, for 30 minutes 6 times for 48 hours postoperatively. Pain scores, measured by the COMFORTneo Scale, and salivary cortisol levels were compared. RESULTS: Although pain scores decreased after surgery in all subjects, no statistically significant difference was observed between the 2 groups (P = .937). There was a significant difference between pre- and postintervention pain scores in the intervention group only (P = .006). Salivary cortisol levels decreased after intervention in the intervention group, but there was no significant difference between pre- and postintervention levels in the 2 groups (P = .716). IMPLICATIONS FOR PRACTICE: Given the reduction in pain scores and salivary cortisol concentrations after white noise intervention, white noise shows potential as an adjunctive soothing measure for neonates after surgery. IMPLICATIONS FOR RESEARCH: Future studies are needed to confirm the efficacy and utility of white noise intervention in clinical settings.

Creating Remarkably Moisture- and Air-Stable Macromolecular Lewis Acid by Integrating Borane within the Polymer Chain: A Highly Active Catalyst for Homo(co)polymerization of Epoxides.

Borane-based Lewis acids (LA) play an indispensable role in the Lewis pair (LP) mediated polymerization. However, most borane-based LPs are moisture- and air-sensitive. Therefore, development of moisture and air-stable borane-based LP is highly desirable. To achieve this goal, the concept of "aggregation induced enlargement effects" by chemically linking multiple borane within a nanoscopic confinement was conceived to create macromolecular LA. Accordingly, an extremely moisture and air stable macromolecular borane, namely, PVP-1B featuring poly(4-vinylphenol) backbone, was constructed. The concentration of borane active site is greatly higher than average concentration due to local confinement. Therefore, an enhanced activity was observed. Moreover, the local LA aggregation effects allow its tolerance to air and large amount of chain transfer agent. Consequently, PVP-1B showed remarkable efficiency for propylene oxide (PO) polymerization at 25 °C (TOF=27900 h-1 ). Furthermore, it enables generation of well-defined telechelic poly (CHO-alt-CO2 ) diol (0.6-15.3 kg/mol) with narrow Ds via copolymerizing cyclohexene oxide and CO2 at 80 °C. This work indicates unifying multiple borane within a polymer in a macromolecular level shows superior catalytic performance than constructing binary, bi(multi)functional systems in a molecular level. This paves a new way to make functional polyethers.

A cluster of transcripts identifies a transition stage initiating leafy head growth in heading morphotypes of Brassica.

Leaf heading is an important and economically valuable horticultural trait in many vegetables. The formation of a leafy head is a specialized leaf morphogenesis characterized by the emergence of the enlarged incurving leaves. However, the transcriptional regulation mechanisms underlying the transition to leaf heading remain unclear. We carried out large-scale time-series transcriptome assays covering the major vegetative growth phases of two headingBrassica crops, Chinese cabbage and cabbage, with the non-heading morphotype Taicai as the control. A regulatory transition stage that initiated the heading process is identified, accompanied by a developmental switch from rosette leaf to heading leaf in Chinese cabbages. This transition did not exist in the non-heading control. Moreover, we reveal that the heading transition stage is also conserved in the cabbage clade. Chinese cabbage acquired through domestication a leafy head independently from the origins of heading in other cabbages; phylogenetics supports that the ancestor of all cabbages is non-heading. The launch of the transition stage is closely associated with the ambient temperature. In addition, examination of the biological activities in the transition stage identified the ethylene pathway as particularly active, and we hypothesize that this pathway was targeted for selection for domestication to form the heading trait specifically in Chinese cabbage. In conclusion, our findings on the transcriptome transition that initiated the leaf heading in Chinese cabbage and cabbage provide a new perspective for future studies of leafy head crops.

Kinetics-Driven Dual Hydrogen Spillover Effects for Ultrasensitive Hydrogen Sensing.

Palladium (Pd)-modified metal oxide semiconductors (MOSs) gas sensors often exhibit unexpected hydrogen (H2 ) sensing activity through a spillover effect. However, sluggish kinetics over a limited Pd-MOS surface seriously restrict the sensing process. Here, a hollow Pd-NiO/SnO2 buffered nanocavity is engineered to kinetically drive the H2 spillover over dual yolk-shell surface for the ultrasensitive H2 sensing. This unique nanocavity is found and can induce more H2 absorption and markedly improve kinetical H2 ab/desorption rates. Meanwhile, the limited buffer-room allows the H2 molecules to adequately spillover in the inside-layer surface and thus realize dual H2 spillover effect. Ex situ XPS, in situ Raman, and density functional theory (DFT) analysis further confirm that the Pd species can effectively combine H2 to form Pd-H bonds and then dissociate the hydrogen species to NiO/SnO2 surface. The final Pd-NiO/SnO2 sensors exhibit an ultrasensitive response (0.1-1000 ppm H2 ) and low actual detection limit (100 ppb) at the operating temperature of 230 °C, which surpass that of most reported H2 sensors.

A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres.

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near-complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near-complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.

A complex locus regulates highly lobed-leaf formation in Brassica juncea.

KEY MESSAGE: Lineage-specific evolution of RCO was described in Brassicaceae. BjRCO.1 and BjRCO.2 within the complex locus regulated highly lobed-leaf formation in Brassica juncea. RCO regulates the formation of lobed leaves in Brassicaceae species. RCO originated from the duplication of LMI1-type sequences and evolved through gene duplication and loss within the Brassicaceae. However, the evolutionary process and diversification of RCO in different lineages of Brassicaceae remain unclear. Although the RCO locus in B. juncea has been associated with lobed-leaf formation, its complexity has remained largely unknown. This study involved the identification of 55 LMI1-like genes in 16 species of Brassicaceae through syntenic analysis. We classified these LMI1-like genes into two types, namely LMI1-type and RCO-type, based on their phylogenetic relationship. Additionally, we proposed two independent lineage-specific evolution routes for RCO following the divergence of Aethionema. Our findings revealed that the LMI1-like loci responsible for lobed-leaf formation in Brassica species are located on the LF subgenomes. For B. juncea (T84-66V2), we discovered that the complex locus underwent duplication through segments of nucleic acid sequence containing Exostosin-LMI1-RCO (E-R-L), resulting in the tandem presence of two RCO-type and two LMI1-type genes on chromosome A10. As additional evidence, we successfully mapped the complex locus responsible for highly lobed-leaf formation to chromosome A10 using a B. juncea F2 population, which corroborated the results of our evolutionary analysis. Furthermore, through transcriptome analysis, we clarified that BjRCO.1 and BjRCO.2 within the complex locus are functional genes involved in the regulation of highly lobed-leaf formation. The findings of this study offer valuable insights into the regulation of leaf morphology for the breeding of Brassica crops.

LSD1 regulates the expressions of core cardiogenic transcription factors and cardiac genes in oxygen and glucose deprivation injured mice fibroblasts in vitro.

Cardiac reprogramming has emerged as a novel therapeutic approach to regenerating the damaged heart by directly converting endogenous cardiac fibroblasts (CFs) into induced cardiomyocytes (iCMs). Cardiac reprogramming requires the activation of the cardiogenic transcriptional program in concert with the repression of the fibroblastic transcriptional program. Lysine-specific demethylase 1 (LSD1) plays an instrumental role in many physiological processes such as cell growth, differentiation and metabolism. The epigenetic modifications of histones are essential for the accurate expression of genes in cardiomyocytes and the normal functioning of the heart. However, the effect of LSD1 in regulating the cardiogenic transcriptional program under myocardial ischemia/reperfusion (I/R) injury remains unclear. Thus, mice I/R injury was induced by 4 and 24 h reperfusion after 1-h occlusion of the left anterior descending coronary artery. The primary CFs and CMs were exposed under oxygen and glucose deprivation (OGD) to mimic I/R injury. The expression of LSD1 significantly decreased in I/R injured heart tissue and OGD-injured primary CFs and CM, and methylated histone presented a notable increase in OGD-injured primary CFs. Overexpression of LSD1 inhibited the injury of primary CFs induced by OGD, but showed limited inhibition on injured primary CMs. Under the OGD condition, LSD1 overexpression significantly increased cell viability, decreased cell apoptosis and reactive oxygen species (ROS) production of primary CFs. The expression of core cardiogenic transcription factors and cardiac genes were significantly decreased in OGD injured primary CFs, whereas LSD1 overexpression reversed the decrease of transcription factors and cardiac genes under the OGD condition. In conclusion, the overexpression of LSD1 has a protective role in I/R injury by inhibiting the histone methylation of primary CFs and regulates the expressions of core cardiogenic transcription factors and cardiac genes, which can prove to be a potential approach for direct cardiac reprogramming.

Nitratireductor luteus sp. nov. isolated from saline-alkali land.

The Gram-staining negative, oxidase and catalase negative strain KC-ST17T, isolated from saline-alkali land, was characterized using a polyphasic approach to determine its taxonomic position. Using 16S rRNA gene sequence analysis, the highest similarity of strain KC-ST17T was found with Nitratireductor pacificus CCTCC AB 209302T (97.2%). Cells are aerobic, non-motile, and rod-shaped. The isolate was found to be able to grow in NaCl concentrations of 0-4.0%. The assembled genome of strain KC-ST17T had a total length of 4.9 Mb with a G + C content of 62.7%. According to genome analysis, strain KC-ST17T encodes genes involved in the reduction of nitrate to nitrite, which may play a role in the utilization of nitrogenous compounds from the soil as an immediate source of energy. Based on the phenotypic characteristics and phylogenetic analysis, strain KC-ST17T was confirmed to represent a novel species in the Nitratireductor genus; thus, the name Nitratireductor luteus sp. nov. was proposed. The type strain of this species was KC-ST17T (= KCTC 92119T = MCCC 1K07309T).

GPR30 Alleviates Pressure Overload-Induced Myocardial Hypertrophy in Ovariectomized Mice by Regulating Autophagy.

The incidence of heart failure mainly resulting from cardiac hypertrophy and fibrosis increases sharply in post-menopausal women compared with men at the same age, which indicates a cardioprotective role of estrogen. Previous studies in our group have shown that the novel estrogen receptor G Protein Coupled Receptor 30 (GPR30) could attenuate myocardial fibrosis caused by ischemic heart disease. However, the role of GPR30 in myocardial hypertrophy in ovariectomized mice has not been investigated yet. In this study, female mice with bilateral ovariectomy or sham surgery underwent transverse aortic constriction (TAC) surgery. After 8 weeks, mice in the OVX + TAC group exhibited more severe myocardial hypertrophy and fibrosis than mice in the TAC group. G1, the specific agonist of GPR30, could attenuate myocardial hypertrophy and fibrosis of mice in the OVX + TAC group. Furthermore, the expression of LC3II was significantly higher in the OVX + TAC group than in the OVX + TAC + G1 group, which indicates that autophagy might play an important role in this process. An in vitro study showed that G1 alleviated AngiotensionII (AngII)-induced hypertrophy and reduced the autophagy level of H9c2 cells, as revealed by LC3II expression and tandem mRFP-GFP-LC3 fluorescence analysis. Additionally, Western blot results showed that the AKT/mTOR pathway was inhibited in the AngII group, whereas it was restored in the AngII + G1 group. To further verify the mechanism, PI3K inhibitor LY294002 or autophagy activator rapamycin was added in the AngII + G1 group, and the antihypertrophy effect of G1 on H9c2 cells was blocked by LY294002 or rapamycin. In summary, our results demonstrate that G1 can attenuate cardiac hypertrophy and fibrosis and improve the cardiac function of mice in the OVX + TAC group through AKT/mTOR mediated inhibition of autophagy. Thus, this study demonstrates a potential option for the drug treatment of pressure overload-induced cardiac hypertrophy in postmenopausal women.

Hierarchical Lotus-Seedpod-Derived Porous Activated Carbon Encapsulated with NiCo2S4 for a High-Performance All-Solid-State Asymmetric Supercapacitor.

Converting biowaste into carbon-based supercapacitor materials provides a new solution for high-performance and environmentally friendly energy storage applications. Herein, the hierarchical PAC/NiCo2S4 composite structure was fabricated through the combination of activation and sulfuration treatments. The PAC/NiCo2S4 electrode garnered advantages from its hierarchical structure and hollow architecture, resulting in a notable specific capacitance (1217.2 F g-1 at 1.25 A g-1) and superior cycling stability. Moreover, a novel all-solid-state asymmetric supercapacitor (ASC) was successfully constructed, utilizing PAC/NiCo2S4 as the cathode and PAC as the anode. The resultant device exhibited exceptionally high energy (49.7 Wh kg-1) and power density (4785.5 W kg-1), indicating the potential of this biomass-derived, hierarchical PAC/NiCo2S4 composite structure for employment in high-performance supercapacitors.

Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica.

Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions. To investigate the potential importance of distant contacts, we performed high-throughput chromatin conformation capture (Hi-C) experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea. We then combined our results with published Hi-C data from Arabidopsis thaliana. We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene. Genes with higher numbers of conserved noncoding sequences (CNSs) nearby were more likely to have contact with distant genes. With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity. In addition, for the genes we studied, distant contacting genes with CNSs were more likely to be transcriptionally coordinated. These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors, correlating with distant contacts to ensure coordinated expression. This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.

Synthesis of Sequence-specific Poly(ester-carbonate) Copolymers via Chemoselective Terpolymerization Controlled by the Stoichiometric Ratio of Phosphazene/Triethylborane.

Chemoselective terpolymerization can produce polymer materials with diverse compositions and sequential structures, and thus have attracted considerable attention in the field of polymer synthesis. However, the intrinsic complexity of three-component system also brings great chanllenge, in regard to the reactivity and selectivity of different monomers. Herein, we report the terpolymerization of CO2 /epoxide/anhydride by a binary organocatalytic C3 N3 -Py-P3 /TEB (triethylborane) system. Both the activity and chemoselectivity were highly dependent upon the molar ratio of C3 N3 -Py-P3 to TEB, and sequence-controlled poly(ester-carbonate) copolymers were readily synthesized through one-pot/one-step methodology by tuning the stoichiometric ratio of phosphazene/TEB. In particular, C3 N3 -Py-P3 /TEB with a molar ratio of 1/0.5 exhibited an unprecedentedly high chemoselectivity for ring-opening alternating copolymerization (ROAC) of cyclohexene oxide (CHO) and phthalic anhydride (PA) first and then ROAC of CO2 /CHO. Thus, well-defined triblock polycarbonate-b-polyester-b-polycarbonate copolymers can be produced from the mixture of CO2 , CHO and PA using a bifunctional initiator. With C3 N3 -Py-P3 /TEB=1/1, tapered copolymers were obtained, while random copolymers with high content of polycarbonate (PC) were synthesized with further increasing the amount of TEB. The mechanism of the unexpected chemoselectivity was further investigated by DFT calculations.

Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa.

Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.

Correlation-based transceiver in-phase/ quadrature skew in-field calibration in dual-polarization coherent optical transmission system.

In this paper, we propose a novel transceiver in-phase/quadrature (I/Q) skew in-field calibration scheme with correlation-based method for the dual-polarization coherent optical system. Simultaneous dual-polarization calibration of transceiver I/Q skews after fiber transmission is experimentally performed. Rx/Tx correlation-based skew estimations (CBSEs) are proposed to accurately estimate the transceiver I/Q skews with dual-polarization OFDM signal. By simulation, the robustness of the Rx/Tx CBSEs is investigated against various transceiver I/Q imbalances and channel impairments including carrier frequency offset (CFO), phase noise (PN), and chromatic dispersion (CD). The simultaneous measurement of large transceiver skews is studied within a range of ±128 ps. The bit error rate (BER) improvement brought by the CBSEs is studied in 80 km single-mode fiber (SMF) transmissions under various Rx/Tx skews. In the experiments, the Rx/Tx skew is measured in the range of 1 to 128 ps w/ and w/o the presence of 5 ps Tx/Rx skew. Simultaneous dual-polarization measurements are performed with the X/Y polarization Tx/Rx skews set to 2.5 ps, 5 ps, 7.5 ps and 10 ps, respectively. The measurement errors are within ±0.2 ps. The 80 km SMF dual-polarization transmission after in-field calibration for inter-data center interconnection (inter-DCI) is implemented, with a data rate of 400 Gb/s for both 16QAM and 32QAM modulation formats.