Origin and evolution of the triploid cultivated banana genome

DATA AVAILABILITY : Genome assemblies of Cavendish, Gros Michel and Zebrina v2.0 have been deposited into NCBI under GenBank numbers JAVVNX000000000, JAVVNW000000000 and JAVVNV000000000 and in the National Genomics Data Center BioProject database (https://ngdc.cncb.ac.cn/bioproject/) under the accession number PRJCA019650. Genome assemblies with annotations and results of ChIP–seq and DNase-seq can be accessed at FigShare (https://figshare.com/projects/Origin_and_evolution_of_the_triploid_cultivated_banana_genome/178041). Raw data used for the assemblies, including PacBio, Illumina and Hi-C data, are available through the Sequence Read Archive of the National Centre for Biotechnology Information (NCBI) under the BioProject PRJNA1017453 with SRA accessions from SRR23425440 to SRR23425472 and from SRR23885547 to SRR23885549. Fifty-eight RNA-seq datasets were downloaded from NCBI BioProject accessions PRJNA381300, PRJNA394594 and PRJNA598018. DNA methylation data were downloaded from NCBI BioProject PRJNA381300.Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.The National Natural Science Foundation of China, Construction of Plateau Discipline of Fujian Province, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program and from Ghent University (Methusalem funding).http://www.nature.com/ng2024-06-11hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-02:Zero Hunge

MicroRNA Transcriptomic Analysis of Heterosis during Maize Seed Germination

Heterosis has been utilized widely in the breeding of maize and other crops, and plays an important role in increasing yield, improving quality and enhancing stresses resistance, but the molecular mechanism responsible for heterosis is far from clear. To illustrate whether miRNA-dependent gene regulation is responsible for heterosis during maize germination, a deep-sequencing technique was applied to germinating embryos of a maize hybrid, Yuyu22, which is cultivated widely in China and its parental inbred lines, Yu87-1 and Zong3. The target genes of several miRNAs showing significant expression in the hybrid and parental lines were predicted and tested using real-time PCR. A total of 107 conserved maize miRNAs were co-detected in the hybrid and parental lines. Most of these miRNAs were expressed non-additively in the hybrid compared to its parental lines. These results indicated that miRNAs might participate in heterosis during maize germination and exert an influence via the decay of their target genes. Novel miRNAs were predicted follow a rigorous criterion and only the miRNAs detected in all three samples were treated as a novel maize miRNA. In total, 34 miRNAs belonged to 20 miRNA families were predicted in germinating maize seeds. Global repression of miRNAs in the hybrid, which might result in enhanced gene expression, might be one reason why the hybrid showed higher embryo germination vigor compared to its parental lines

Epidemic spreading in community networks

Social networks have the structure of communities. To understand how the community structure affects epidemic spreading, we present a simplified model of community network, and investigate the epidemic propagation in this model. We find that, compared to the random network, the community network has a broader degree distribution, a smaller threshold of epidemic outbreak, and more prevalence to keep the outbreak endemic. The formulae of epidemic threshold are given and confirmed by numerical simulations

Detection of phase locking from non-stationary time series

The detection of the interrelation between non-stationary time series is a key problem unsolved in the analysis of practical data. Here we present a novel approach to detect the phase locking of time series in non-stationary status, which does not need the reconstruction of the attractor but gets information from the consistence of local rotation speeds. This method can be conveniently used for practical situations, such as the epileptic seizure

A simple, flexible and automatic 3D calibration method for a phase calculation-based fringe projection imaging system

An important step of phase calculation-based fringe projection systems is 3D calibration, which builds up the relationship between an absolute phase map and 3D shape data. The existing 3D calibration methods are complicated and hard to implement in practical environments due to the requirement of a precise translating stage or gauge block. This paper presents a 3D calibration method which uses a white plate with discrete markers on the surface. Placing the plate at several random positions can determine the relationship of absolute phase and depth, as well as pixel position and X, Y coordinates. Experimental results and performance evaluations show that the proposed calibration method can easily build up the relationship between absolute phase map and 3D shape data in a simple, flexible and automatic way

Pre-synthesis resource generation and estimation for transport-triggered architecture (TTA)-like architecture

Electronic system level (ESL) design is widely adopted in today's embedded systems development projects to cope with increasing system complexity and shrinking time-to-market. Even though functional verification can be performed at the system level and early design stage efficiently, it is still difficult to perform accurate hardware resource estimation. In this paper, we consider the problem of mapping an input high-level algorithm in C into hardware implementation based on the transport-triggered architecture (TTA)-like architecture, and present effective techniques for predicting architectural-level parameters and gate-level resource consumption without going through the lengthy hardware synthesis process in order to facilitate rapid design space exploration. We use some common DSP algorithms and a complete industry GPS application to show that our resource estimation results match the actual results from hardware synthesis very well, and they can be used in a feedback loop to optimize the input algorithm specification in C, e.g., the total gate count of the GPS application is reduced by 25\% compared to the original input algorithm specification. In addition, the simulation results of the generated hardware descriptions in Verilog also show good agreement with the execution results of the original GPS program in C. (C) 2008 Elsevier B.V. All rights reserved

Tripsense : a trust-based vehicular platoon crowdsensing scheme with privacy preservation in VANETs

In this paper, we propose a trust-based vehicular platoon crowdsensing scheme, named TripSense, in VANET. The proposed TripSense scheme introduces a trust-based system to evaluate vehicles’ sensing abilities and then selects the more capable vehicles in order to improve sensing results accuracy. In addition, the sensing tasks are accomplished by platoon member vehicles and preprocessed by platoon head vehicles before the data are uploaded to server. Hence, it is less time-consuming and more efficient compared with the way where the data are submitted by individual platoon member vehicles. Hence it is more suitable in ephemeral networks like VANET. Moreover, our proposed TripSense scheme integrates unlinkable pseudo-ID techniques to achieve PM vehicle identity privacy, and employs a privacy-preserving sensing vehicle selection scheme without involving the PM vehicle’s trust score to keep its location privacy. Detailed security analysis shows that our proposed TripSense scheme not only achieves desirable privacy requirements but also resists against attacks launched by adversaries. In addition, extensive simulations are conducted to show the correctness and effectiveness of our proposed scheme.Published versio