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| 1 | The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize显示文摘Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequeneed maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZSrelated lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity.by.descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we dem on strated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function.related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize. | Chunhui Li Wei Song Yingfeng Luo Shenghan Gao Ruyang Zhang Zi Shi Xiaqing Wang Ronghuan Wang Fengge Wang Jidong Wang Yanxin Zhao Aiguo Su Shuai Wang Xin Li Meijie Luo Shuaishuai Wang Yunxia Zhang Jianrong Ge Xinyu Tan Ye Yuan Xiaochun Bi Hang He Jianbing Yan Yuandong Wang Songnian Hu Jiuran Zhao | 2019 | Molecular Plant2019，12，3： | 15 |
| 2 | The apricot(Prunus armeniaca L.)genome elucidates Rosaceae evolution and beta-carotenoid synthesis显示文摘Apricots,scientifically known as Prunus armeniaca L,are drupes that resemble and are closely related to peaches or plums.As one of the top consumed fruits,apricots are widely grown worldwide except in Antarctica.A high-quality reference genome for apricot is still unavailable,which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background,evolutionary diversity,and population diversity in apricot.DNA from P.armeniaca was used to generate a standard,size-selected library with an average DNA fragment size of~20 kb.The library was run on Sequel SMRT Cells,generating a total of 16.54 Gb of PacBio subreads(N50=13.55 kb).The high-quality P.armeniaca reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70×coverage and 171×Illumina reads(40.46 Gb),combined with a genetic map for chromosome scaffolding.The assembled genome size was 221.9 Mb,with a contig NG50 size of 1.02 Mb.Scaffolds covering 92.88%of the assembled genome were anchored on eight chromosomes.Benchmarking Universal Single-Copy Orthologs analysis showed 98.0%complete genes.We predicted 30,436 protein-coding genes,and 38.28%of the genome was predicted to be repetitive.We found 981 contracted gene families,1324 expanded gene families and 2300 apricot-specific genes.The differentially expressed gene(DEG)analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase(NCED)gene but not lycopene beta-cyclase(LcyB)gene results in a lowβ-carotenoid content in the white cultivar“Dabaixing”.This complete and highly contiguous P.armeniaca reference genome will be of help for future studies of resistance to plum pox virus(PPV)and the identification and characterization of important agronomic genes and breeding strategies in apricot. | Fengchao Jiang Junhuan Zhang Sen Wang Li Yang Yingfeng Luo Shenghan Gao Meiling Zhang Shuangyang Wu Songnian Hu Haoyuan Sun Yuzhu Wang | 2019 | Horticulture Research2019，6，1： | 9 |
| 3 | LiPO_(2)F_(2) electrolyte additive for high-performance Li-rich cathode material显示文摘Li-rich layered oxide cathodes have received considerable attention because of the high operating potential and specific capacity. However, the structural instability and parasitic reactions at high potential cause severe degradation of the electrochemical performance. In our studies, the cycling stability of Li_(1.14)Ni_(0.133)Co_(0.133)Mn_(0.544)O_(2) cathode is improved with LiPO_(2)F_(2) electrolyte additive. After 500 cycles, the capacity retention is increased from 53.6% to 85% at 3 C by LiPO_(2)F_(2) modification. This performance is mainly attributed to the enhanced interfacial stability of the Li-rich cathode. Based on systematic characterization, LiPO_(2)F_(2) additive was found to promote a stable interface film on the cathode surface during the cycling and mitigates the interfacial side reactions. This study provides new insights for improving high-potential Li-rich layered oxide batteries. | Bing Jiang Jingru Li Bi Luo Qizhang Yan Hao Li Lehao Liu Lihua Chu Yingfeng Li Qiaobao Zhang Meicheng Li | 2021 | Journal of Energy Chemistry2021，30，9： | 3 |
| 4 | BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data显示文摘The emergence of next-generation sequencing (NGS) technologies has significantly improved sequencing throughput and reduced costs. However, the short read length, duplicate reads and massive volume of data make the data processing much more difficult and complicated than the first-generation sequencing technology. Although there are some software packages developed to assess the data quality, those packages either are not easily available to users or require bioinformatics skills and computer resources. Moreover, almost all the quality assessment software currently available didn't taken into account the sequencing errors when dealing with the duplicate assessment in NGS data. Here, we present a new user-friendly quality assessment software package called BIGpre, which works for both Illumina and 454 platforms. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well. BIGpre is primarily written in Perl and integrates graphical capability from the statistics package R. This package produces both tabular and graphical summaries of data quality for sequencing datasets from Illumina and 454 platforms. Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http://gffzz3d42f7e793a54046hqc60xcu9955p6bqw.ffgz.tsg.suse.edu.cn/. | Tongwu Zhang Yingfeng Luo Kan Liu Linlin Pan Bing Zhang Jun Yu Songnlan Hu | 2011 | Genomics, Proteomics & Bioinformatics2011，9，6： | 3 |
| 5 | Two-stage hybrid batching flowshop scheduling with blocking and machine availability constraints using genetic algorithm显示文摘 | Luo Hao Huang G Q Zhang Yingfeng | 2009 | Robotics and Computer Integrated Manufacturing2009，25，： | 1 |
| 6 | Two-stage hy- brid batching flowshop scheduling with blocking and ma- chine availability constraints using genetic algorithm 显示文摘 | HAO Luo GEORGE Q HUANG Yingfeng | 2009 | Robotics and Computer Integrated Manufacturing2009，25，： | 1 |
| 7 | Development of an Agrobacterium-mediated CRISPR/Cas9 system in pea(Pisum sativum L.)显示文摘Pea(Pisum sativum L.)is an annual cool-season legume crop.Owing to its role in sustainable agriculture as both a rotation and a cash crop,its global market is expanding and increased production is urgently needed.For both technical and regulatory reasons,neither conventional nor transgenic breeding techniques can keep pace with the demand for increased production.In answer to this challenge,CRISPR/Cas9 genome editing technology has been gaining traction in plant biology and crop breeding in recent years.However,there are currently no reports of the successful application of the CRISPR/Cas9 genome editing technology in pea.We developed a transient transformation system of hairy roots,mediated by Agrobacterium rhizogenes strain K599,to validate the efficiency of a CRISPR/Cas9 system.Further optimization resulted in an efficient vector,PsU6.3-tRNA-PsPDS3-en35S-PsCas9.We used this optimized CRISPR/Cas9 system to edit the pea phytoene desaturase(PsPDS)gene,causing albinism,by Agrobacterium-mediated genetic transformation.This is the first report of successful generation of gene-edited pea plants by this route. | Guan Li Rong Liu Rongfang Xu Rajeev KVarshney Hanfeng Ding Mengwei Li Xin Yan Shuxian Huang Juan Li Dong Wang Yishan Ji Chenyu Wang Junguang He Yingfeng Luo Shenghan Gao Pengcheng Wei Xuxiao Zong Tao Yang | 2023 | The Crop Journal2023，11，1： | 0 |
| 8 | Application and Hydration Resistance of SiC Refractories for Water-cooled Wall of Waste Incinerators显示文摘According to the dual needs of heat transfer and thermal insulation in incinerators,different parts of the incinerators are designed with refractories of different SiC contents.Water vapor is mainly concentrated in the zones of feeding,drying and combustion,and the main damage factors of SiC refractories include high temperature and hydration.The results of hydration resistance of typical SiC-containing refractories show that the higher the SiC content,the worse the hydration resistance.Si_(3)N_(4)-SiC refractories after oxidation treatment have good hydration corrosion resistance,which are appropriate for water-cooled wall of waste incinerators. | LUO Huaming CAI Binli YUAN Zhenqiang ZUO Genliang Zhang Jingzheng WANG Fengyu LI Jinyu WEI Yingfeng SUN Huochang ZHAN Huasheng | 2022 | China's Refractories2022，31，2： | 0 |
| 9 | Integrated Metabolomics and Transcriptomics Analyses Reveal Metabolic Landscape in Neuronal Cells during JEV Infection显示文摘Japanese encephalitis virus(JEV) is a leading cause of viral encephalitis in endemic regions of Asia. The neurotropism of JEV and its high-efficiency replication in neurons are the key events for pathogenesis. Revealing the interplay between virus and host cells in metabolic facet is of great importance both for unraveling the pathogenesis mechanisms and providing novel antiviral targets. This study took advantage of the integration analysis of metabolomics and transcriptomics to depict the metabolic profiles of neurons during the early stage of JEV infection. Increased glycolysis and its branched pentose phosphate pathway(PPP) flux and impaired oxidative phosphorylation(OXPHOS) in glucose utilization,and the catabolic patterns of lipid metabolism were created to facilitate the biosynthesis of precursors needed for JEV replication in neurons. Pharmacological inhibitions of both glycolysis pathway and PPP in neurons suggested its indispensable role in maintaining the optimal propagation of JEV. In addition, analysis of metabolomic-transcriptomic regulatory network showed the pivotal biological function of lipid metabolism during JEV infection. Several pro-inflammatory lipid metabolites were significantly up-regulated and might partially be responsible for the progression of encephalitis.These unique metabolic reprogramming features might give deeper insight into JEV infected neurons and provide promising antiviral approaches targeting metabolism. | Mengyuan Li Jiali Yang Chuantao Ye Peiyu Bian Xiaofei Yang Haijun Zhang Chuanyu Luo Zhifeng Xue Yingfeng Lei Jianqi Lian | 2021 | Virologica Sinica2021，36，6： | 0 |
| 10 | Correction to: Integrated Metabolomics and Transcriptomics Analyses Reveal Metabolic Landscape in Neuronal Cells During JEV Infection显示文摘Correction to:Virologica Sinica http://gffzzd3cc09b8251d45dfsqc60xcu9955p6bqw.ffgz.tsg.suse.edu.cn/10.1007/s12250-021-00445-0 In the original version of this article,one image in Fig.4 was accidently duplicated during figure layout and the dilution rate was mislabeled. | Mengyuan Li Jiali Yang Chuantao Ye Peiyu Bian Xiaofei Yang Haijun Zhang Chuanyu Luo Zhifeng Xue Yingfeng Lei Jianqi Lian | 2021 | Virologica Sinica2021，36，6： | 0 |
| 11 | Development of the expressed immunoglobulinμchain repertoire during maturation of mice B cells显示文摘In the bone marrow and spleen,the developing B cell populations undergo both negative and positive selections to shape their B cell receptor repertoire.To gain insight into the shift of the immunoglobulin heavy(IgH)chain repertoire during B cell development,we undertook large scale Igμchain repertoire analysis of pre-B,immature B and spleen B cell populations.We found that the majority of VH gene segments,VH families,JH and D gene segments,were observed to have significantly different usage frequencies when three B cell populations were compared,but the usage profile of the VH,D,and JH genes between different B cell populations showed high correlations.In both productive and nonproductive rearrangements,the length of CDRH3 shortened significantly on average when B cells entered the periphery.However,the CDRH3 length distribution of nonproductive rearrangements did not follow a Gaussian distribution,but decreased successively in the order 3n–2,3n–1 and 3n,suggesting a direct correlation between mRNA stability and CDRH3 length patterns of nonproductive rearrangements.Further analysis of the individual components comprising CDRH3 of productive rearrangements indicated that the decrease in CDRH3 length was largely due to the reduction of N addition at the 5′and 3′junctions.Moreover,with development,the amino acid content of CDRH3 progressed toward fewer positively charged and nonpolar residues but more polar residues.All these data indicated that the expressed Igμchain repertoire,especially the repertoire of CDRH3,was fine-tuned when B cells passed through several checkpoints of selection during the process of maturation. | Jingwen LIANG Yingfeng LUO Yi SUN Meng LEI Bing ZHANG Songnian HU Yaofeng ZHAO | 2014 | Frontiers of Agricultural Science and Engineering2014，1，3： | 0 |
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