Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system

The Atlantic salmon genome provides insights into rediploidization

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.publishedVersio

Exome Sequencing Identifies ZNF644 Mutations in High Myopia

Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3′UTR+12 C>G, and 3′UTR+592 G>A) in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE). Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form

The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. © 2012 Macmillan Publishers Limited. All rights reserved

Video Fire Detection Algorithm using Multi-Feature Fusion

At present, the moving target detection and flame characteristics extraction almost become the most important parts in majority of video fire detection systems. Through the above two-part study, a new fire features detection method is presented in precise moving target area. That is, using the improved background difference method and flame features (such as the color and uniformity, Wavelet energy, stroboscopic and contour features) to detect fire. Experiments show that this method can improve theaccuracy and anti-interference ability of fire detection. DOI: http://dx.doi.org/10.11591/telkomnika.v11i10.334

Nonreversible Enhanced Crystallization of Olefin Block Copolymer Induced by Preshearing

In this work, the influence of preshearing on crystallization of olefin block copolymer (OBC) was systematically investigated. It was found that upon an interval of melt preshear the crystallization rate of OBC was prominently elevated which was evidenced by both nonisothermal and isothermal crystallization results. The lamellar thickness of OBC increased and the size of spherulites decreased after shear. Interestingly, annealing and multiple heating and cooling experiments demonstrated that the enhancement effect on crystallization was nonreversible. The morphology observations suggested that preshearing caused an alteration in mesophase structure of OBC. On the basis of our results, we speculated that the increase in the amount of hard blocks that dissolved in the soft-block-rich matrix induced by shear promoted the unique “pass-through” crystallization process of OBC, which should be responsible for the largely enhanced crystallization of sheared OBC

Security Service Function Chain Based on Graph Neural Network

With the rapid development and wide application of cloud computing, security protection in cloud environment has become an urgent problem to be solved. However, traditional security service equipment is closely coupled with the network topology, so it is difficult to upgrade and expand the security service, which cannot change with the change of network application security requirements. Building a security service function chain (SSFC) makes the deployment of security service functions more dynamic and scalable. Based on a software defined network (SDN) and network function virtualization (NFV) environment, this paper proposes a solution to the particularity optimization algorithm of network topology feature extraction using graph neural network. The experimental results show that, compared with the shortest path, greedy algorithm and hybrid bee colony algorithm, the average success rate of the graph neural network algorithm in the construction of the security service function chain is more than 90%, far more than other algorithms, and far less than other algorithms in construction time. It effectively reduces the end-to-end delay and increases the network throughput

Security Service Function Chain Based on Graph Neural Network

With the rapid development and wide application of cloud computing, security protection in cloud environment has become an urgent problem to be solved. However, traditional security service equipment is closely coupled with the network topology, so it is difficult to upgrade and expand the security service, which cannot change with the change of network application security requirements. Building a security service function chain (SSFC) makes the deployment of security service functions more dynamic and scalable. Based on a software defined network (SDN) and network function virtualization (NFV) environment, this paper proposes a solution to the particularity optimization algorithm of network topology feature extraction using graph neural network. The experimental results show that, compared with the shortest path, greedy algorithm and hybrid bee colony algorithm, the average success rate of the graph neural network algorithm in the construction of the security service function chain is more than 90%, far more than other algorithms, and far less than other algorithms in construction time. It effectively reduces the end-to-end delay and increases the network throughput

Spatiotemporal Patterns of Cultivated Land Quality Integrated with Multi-Source Remote Sensing : A Case Study of Guangzhou, China

Scientifically revealing the spatiotemporal patterns of cultivated land quality (CLQ) is crucial for increasing food production and achieving United Nations Sustainable Development Goal (SDG) 2: Zero Hunger. Although studies on the evaluation of CLQ have been conducted, an effective evaluation system that is suitable for the macro-regional scale has not yet been developed. In this study, we first defined the CLQ from four aspects: soil fertility, natural conditions, construction level, and cultivated land productivity. Then, eight indicators were selected by integrating multi-source remote sensing data to create a new CLQ evaluation system. We assessed the spatiotemporal patterns of CLQ in Guangzhou, China, from 2010 to 2018. In addition, we identified the main factors affecting the improvement of CLQ. The results showed that the CLQ continuously improved in Guangzhou from 2010 to 2018. The area of high-quality cultivated land increased by 13.7%, which was mainly distributed in the traditional agricultural areas in the northern and eastern regions of Guangzhou. The areas of medium-and low-quality cultivated land decreased by 8.1% and 5.6%, respectively, which were scattered throughout the whole study area. The soil fertility and high productivity capacity were the main obstacle factors that affected the improvement of CLQ. Simultaneously, the obstacle degree of stable productivity capacity gradually increased during the study period. Therefore, the targeted improvement measures could be put forward by applying biofertilizers, strengthening crop management and constructing well-facilitated farmland. The new CLQ evaluation system we proposed is particularly practical at the macro-regional scale, and the results provided targeted guidance for decision makers to improve CLQ and promote food security