|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis显示文摘Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement. | Junyang Yue Qinyao Chen Yingzhen Wang Lei Zhang Chen Ye Xu Wang Shuo Cao Yunzhi Lin Wei Huang He Xian Hongyan Qin Yanli Wang Sijia Zhang Ying Wu Songhu Wang Yi Yue Yongsheng Liu | 2023 | Horticulture Research2023，10，2： | 4 |
| 2 | Parameterizations of different hydrometeor spectral relative dispersion in the convective clouds显示文摘离散度的诊断对模式中沉降过程的准确描述至关重要.本文利用WRF模式结合谱分档方案模拟安徽寿县地区的对流云,研究不同水成物的离散度.首先,无论在清洁还是污染条件下,除冰晶谱的离散度与体积平均直径间呈现负相关关系外,云滴,雨滴,霰粒子与雪粒子谱离散度与体积平均直径呈现正相关关系;云滴和雨滴受碰并过程影响,冰晶,霰粒子和雪粒子分别受凝华过程,淞附过程和聚并增长影响.其次,综合考虑污染与清洁条件下离散度和体积平均直径之间的相关关系,建立了离散度的参数化方案.最后,把该离散度方案应用到下落末速度的参数化方案中,结果表明,对于云滴,冰晶,霰粒子和雪粒子,在Gamma分布中假设谱形参数等于0会低估谱形参数而高估离散度.对于雨滴而言,假设谱形参数等于0与参数化方案结果接近.针对不同的水成物,给出了最合适的谱形参数定值.本文发展的离散度方案为进一步优化模式中下落末速度参数化方案提供参考. | Qinyao Zou Lei Zhu Chunsong Lu Guang J.Zhang Xiaoqi Xu Qian Chen Dan Li | 2022 | Atmospheric and Oceanic Science Letters2022，15，3： | 0 |
| 3 | quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification显示文摘A high-quality genome is the basis for studies on functional,evolutionary,and comparative genomics.The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences,along with the emergence of a new‘telomere-to-telomere(T2T)assembly’era.However,the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited.Here,we developed a user-friendly web toolkit,quarTeT,which currently includes four modules:AssemblyMapper,GapFiller,TeloExplorer,and CentroMiner.First,AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome.Then,GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences.Finally,TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome.These four modules can be used alone or in combination with each other for T2T genome assembly and characterization.As a case study,by adopting the entire modular functions of quarTeT,we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0,which was assembled with the addition of manual handling.Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods.Collectively,quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration. | Yunzhi Lin Chen Ye Xingzhu Li Qinyao Chen Ying Wu Feng Zhang Rui Pan Sijia Zhang Shuxia Chen Xu Wang Shuo Cao Yingzhen Wang Yi Yue Yongsheng Liu Junyang Yue | 2023 | Horticulture Research2023，10，8： | 0 |
| 4 | Observation-based sources evolution of non-methane hydrocarbons (NMHCs) in a megacity of China显示文摘Both concentrations and emissions of many air pollutants have been decreasing due to implement of control measures in China,in contrast to the fact that an increase in emissions of non-methane hydrocarbons(NMHCs)has been reported.This study employed seven years continuous NMHCsmeasurements and the related activities data of Shanghai,a megacity in China,to explore evolution of emissions and effectiveness of air pollution control measures.The mixing ratio of NMHCs showed no statistical interannual changes,of which their compositions exhibited marked changes.This resulted in a decreasing trend of ozone formation potential by 3.8%/year(p<0.05,the same below),which should be beneficial to ozone pollution mitigation as its production in Shanghai is in the NMHCs-limited regime.Observed alkanes,aromatics and acetylene changed by+3.7%/year,-5.9%/year and-7.4%/year,respectively,and alkenes showed no apparent trend.NMHCs sources were apportioned by a positive matrix factorization model.Accordingly,vehicular emissions(-5.9%/year)and petrochemical industry emissions(-7.1%/year)decreased significantly,but the decrease slowed down;significant reduction in solvent usage(-9.0%/year)appeared after 2010;however,emissions of natural gas(+12.6%/year)and fuel evaporation(with an increasing fraction)became more important.The inconsistency between observations and inventories was found in interannual trend and speciation as well as source contributions,emphasizing the need for further validation in NMHCs emission inventory.Our study confirms the effectiveness of measures targeting mobile and centralized emissions from industrial sources and reveals a need focusing on fugitive emissions,which provided new insights into future air policies in polluted region. | Yarong Peng Hongli Wang Qian Wang Shengao Jing Jingyu An Yaqin Gao Cheng Huang Rusha Yan Haixia Dai Tiantao Cheng Qiang Zhang Meng Li Jianlin Hu Zhihao Shi Li Li Shengrong Lou Shikang Tao Qinyao Hu Jun Lu Changhong Chen | 2023 | Journal of Environmental Sciences2023，，2： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员