2021 No. 1

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ARTICLE
Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis
Mao Weitao, Yao Guoxin, Wang Shangde, Zhou Lei, Chen Guosong, Dong Ningguang, Hu Guanglong
2021, 1(1): 1-9. doi: 10.48130/FR-2021-0009
Abstract:
Diospyros lotus L. (Date plum) is an important tree species that produces fruit with a high nutritional value. An accurate chromosomal assembly of a species facilitates research on chromosomal evolution and functional gene mapping. In this study, we assembled the first chromosome-level genomes of seeded and seedless D. lotus using Illumina short reads, PacBio long reads, and Hi-C technology. The assembled genomes comprising 15 chromosomes were 617.66 and 647.31 Mb in size, with a scaffold N50 of 40.72 and 42.67 Mb for the seedless and seeded D. lotus, respectively. A BUSCO analysis revealed that the seedless and seeded D. lotus genomes were 91.53% and 91.60% complete, respectively. Additionally, 20,689 (95.4%) and 22,844 (98.5%) protein-coding genes in the seedless and seeded D. lotus genomes were annotated, respectively. Comparisons of the chromosomes between genomes revealed inversions and translocations on chromosome 8 and inversions on chromosome 11. We identified 490 and 424 gene families that expanded in the seedless and seeded D. lotus, respectively. The enriched pathways among these gene families included the estrogen signaling pathway, the MAPK signaling pathway, and biosynthetic pathways for flavonoids, monoterpenoids, and glucosinolates. Moreover, we constructed the first Diospyros genome database (http://www.persimmongenome.cn). On the basis of our data, we developed the first high-quality annotated D. lotus reference genomes, which will be useful for genomic studies on persimmon and for clarifying the molecular mechanisms underlying important traits. Comparisons between the seeded and seedless D. lotus genomes may also elucidate the molecular basis of seedlessness.
Reviews
Application of Artificial Intelligence Technology to Numerical Weather Prediction
Sun Jian, Cao Zhuo, Li Heng, Qian Simeng, Wang Xin, Yan Limin, Xue Wei
2021, 32(1): 1-11. doi: 10.11898/1001-7313.20210101
Abstract:
Numerical weather prediction technology plays an increasingly important role in improving accuracy and service level of modern weather forecast. With the development of observation system and higher resolution and complexity of the numerical weather prediction model, the products of numerical weather forecast have been greatly improved in quantity and quality, and can offer rich information at high spatial-temporal frequency. However, such a large amount of prediction data are not fully explored. Artificial intelligence has achieved great success in many fields, such as pattern recognition and natural language processing, which provides an opportunity for further improving numerical weather prediction. It's also employed in initialization, numerical model and production of weather forecast service, involving observation system, data assimilation, model integration, ensemble forecast and high-performance computing methods. Both the accuracy of forecast results and computational efficiency have been improved by using error correction, parameter estimation, local surrogate model and so on. In addition, some end-to-end neural network models also show the potential of pure data-driven weather forecast. These models use spatial-temporal observation data as input and directly output the prediction results in terms of deterministic results or probabilities. Some of them perform well in short-term severe convective weather, precipitation, and long-term climate forecast. Existing works employ various artificial intelligence technology methods, mainly including large-scale calculation of neural network, feature analysis, interpretability, and customized loss function. However, there are still some challenges, the potential of artificial intelligence needs to be further explored. Some issues should be carefully considered, including weak interpretability, uncertainty analysis and the coupling with conventional numerical models, and how to use physical knowledge to guide the design of artificial intelligence model is also worth addressing. To deal with these challenges, some promising suggestions are proposed. Bayesian network and causal network will help to establish more comprehensive and profound feature engineering. Using Bayesian inference to generate distribution characteristics of current meteorological states may be an alternative to efficient and effective uncertainty quantification. The development of some standard workflow and framework will contribute to the coupling of conventional numerical model and artificial intelligence module. Successful artificial intelligence applications in weather forecast require deep cooperation between meteorological experts and computer experts who focus on artificial intelligence and high-performance computing.