nearest neighbor (kNN) method is a popular classification method in data mining and statistics because of its simple implementation and significant classification performance. However, it is impractical for traditional kNN methods to assign a fixed value (even though set by experts) to all test samples. Previous solutions assign different values to different test samples by the cross validation method but are usually time-consuming. This paper proposes a kTree method to learn different optimal values for different test/new samples, by involving a training stage in the kNN classification. Specifically, in the training stage, kTree method first learns optimal values for all training samples by a new sparse reconstruction model, and then constructs a decision tree (namely, kTree) using training samples and the learned optimal values. In the test stage, the kTree fast outputs the optimal value for each test sample, and then, the kNN classification can be conducted using the learned optimal value and all training samples. As a result, the proposed kTree method has a similar running cost but higher classification accuracy, compared with traditional kNN methods, which assign a fixed value to all test samples. Moreover, the proposed kTree method needs less running cost but achieves similar classification accuracy, compared with the newly kNN methods, which assign different values to different test samples. This paper further proposes an improvement version of kTree method (namely, k*Tree method) to speed its test stage by extra storing the information of the training samples in the leaf nodes of kTree, such as the training samples located in the leaf nodes, their kNNs, and the nearest neighbor of these kNNs. We call the resulting decision tree as k*Tree, which enables to conduct kNN classification using a subset of the training samples in the leaf nodes rather than all training samples used in the newly kNN methods. This actually reduces running cost of test stage. Finally, the experimental results on 20 real data sets showed that our proposed methods (i.e., kTree and k*Tree) are much more efficient than the compared methods in terms of classification tasks.
CRISPR/Cas9 system can precisely edit genomic sequence and effectively create knockout mutations in T0 generation watermelon plants. Genome editing offers great advantage to reveal gene function and generate agronomically important mutations to crops. Recently, RNA-guided genome editing system using the type II clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) has been applied to several plant species, achieving successful targeted mutagenesis. Here, we report the genome of watermelon, an important fruit crop, can also be precisely edited by CRISPR/Cas9 system. ClPDS, phytoene desaturase in watermelon, was selected as the target gene because its mutant bears evident albino phenotype. CRISPR/Cas9 system performed genome editing, such as insertions or deletions at the expected position, in transfected watermelon protoplast cells. More importantly, all transgenic watermelon plants harbored ClPDS mutations and showed clear or mosaic albino phenotype, indicating that CRISPR/Cas9 system has technically 100% of genome editing efficiency in transgenic watermelon lines. Furthermore, there were very likely no off-target mutations, indicated by examining regions that were highly homologous to sgRNA sequences. Our results show that CRISPR/Cas9 system is a powerful tool to effectively create knockout mutations in watermelon.
The K Nearest Neighbor (kNN) method has widely been used in the applications of data mining and machine learning due to its simple implementation and distinguished performance. However, setting all test data with the same k value in the previous kNN methods has been proven to make these methods impractical in real applications. This article proposes to learn a correlation matrix to reconstruct test data points by training data to assign different k values to different test data points, referred to as the Correlation Matrix kNN (CM-kNN for short) classification. Specifically, the least-squares loss function is employed to minimize the reconstruction error to reconstruct each test data point by all training data points. Then, a graph Laplacian regularizer is advocated to preserve the local structure of the data in the reconstruction process. Moreover, an 1-norm regularizer and an 2,1-norm regularizer are applied to learn different k values for different test data and to result in low sparsity to remove the redundant/noisy feature from the reconstruction process, respectively. Besides for classification tasks, the kNN methods (including our proposed CM-kNN method) are further utilized to regression and missing data imputation. We conducted sets of experiments for illustrating the efficiency, and experimental results showed that the proposed method was more accurate and efficient than existing kNN methods in data-mining applications, such as classification, regression, and missing data imputation.
Chromoplast development plays a crucial role in controlling carotenoid content in watermelon flesh. Modern cultivated watermelons with colorful flesh are believed to originate from pale-colored and no-sweet progenitors. But the molecular basis of flesh color formation and regulation is poorly understood. More chromoplasts and released carotenoid globules were observed in the red-fleshed fruit of the 97103 cultivar than in the pale-colored fruits of the PI296341-FR line. Transcriptome profiles of these two materials identified Cla017962, predicted as ClPHT4;2, was dramatically up-regulated during flesh color formation. High ClPHT4;2 expression levels were closely correlated with increased flesh carotenoid contents among 198 representative watermelon accessions. Down-regulation of ClPHT4;2 expression in transgenic watermelons reduced the fruit carotenoid accumulation. ClPHT4;2 as a function of chromoplast-localized phosophate transporter was tested by heterologous expression into a yeast phosphate-uptake-defective mutant, western blotting, subcellular localization, and immunogold electron microscopy analysis. Two transcription factors, ClbZIP1 and ClbZIP2, were identified, which responded to ABA and sugar signaling to regulate ClPHT4;2 transcription only in cultivated watermelon species. Our findings suggest that elevated ClPHT4;2 gene expression is necessary for carotenoid accumulation, and may help to characterize the co-development of flesh color and sweetness during watermelon development and domestication.
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.
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