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Rice Information GateWay： A Comprehensive Bioinformatics Platform for Indica Rice Genomes

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Molecular Plant 2018年第3期11卷 505-507页

作者： jia-ming,song Yang,Lei Cheng-Cheng,Shu Yuduan,Ding Feng,Xing Hao,Liu jia,Wang Weibo,Xie jianwei,Zhang Ling-Ling,Chen National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 P. R. China Agricultural Bioinformatics Key Laboratory of Hubei Province College of Informatics Huazhong Agricultural University Wuhan 430070 China [∗]Corresponding author [∗∗]Corresponding author

Dear Editor,Oryza sativa subsp, indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Project Database （RAP-DB）（Ohyanagi et al., 2006） and Michigan State University Rice Genome Annotation Project （MSU-RGAP）（Ouyang et al., 2007） are two popular databases that have been developed to manage rice genomic and transcriptomic data based on the unified reference genome of japonica cultivar Nipponbare （International Rice Genome Sequencing Project, 2005）. Beijing Genomics Institute Rice Information System （BGI-RIS）（Zhao et ai., 2004） is an available resource for indica rice cultivar 93-11;

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Two gap-free reference genomes and a global view of the centromere architecture in rice

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Molecular Plant 2021年第10期14卷 1757-1767页

作者： jia-ming song Wen-Zhao Xie Shuo Wang Yi-Xiong Guo Dal-Hoe Koo Dave Kudrna Chenbo Gong Yicheng Huang jia-Wu Feng Wenhui Zhang Yong Zhou Andrea Zuccolo Evan Long Seunghee Lee Jayson Talag Run Zhou Xi-Tong Zhu Daojun Yuan Joshua Udall Weibo Xie Rod AWing Qifa Zhang Jesse Poland jianwei Zhang Ling-Ling Chen National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China College of Life Science and Technology Guangxi UniversityNanning 530004China Wheat Genetics Resource Center Department of Plant PathologyKansas State UniversityManhattanKSUSA Arizona Genomics Institute School of Plant SciencesUniversity of ArizonaTucsonAZ 85721USA Center for Desert Agriculture Biological and Environmental Sciences&Engineering Division(BESE)King Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Saudi Arabia Plant and Wildlife Science Department Brigham Young UniversityProvoUT 84602USA International Rice Research Institute(IRRI) Strategic InnovationLos Baños4031 LagunaPhilippines Crop Germplasm Research Unit USDA-ARS2881 F&B RoadCollege StationTX 77845USA

Rice(Oryza sativa),a major staple throughout the world and a model system for plant genomics and breeding,was the first crop genome sequenced almost two decades ***,reference genomes for all higher organisms to date contain gaps and missing ***,we report the assembly and analysis of gap-free reference genome sequences for two elite *** xian/indica rice varieties,Zhenshan 97 and minghui 63,which are being used as a model system for studying heterosis and ***-free reference genomes provide the opportunity for a global view of the structure and function of *** show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and *** addition,the similarity of CentO repeats in the same chromosome is higher than across chromosomes,supporting a model of local expansion and *** genomes have over 395 non-TE genes located in centromere regions,of which∼41%are actively *** large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two *** availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.

关键词： rice genome ZS97 MH63 hybrid rice centromere architecture

Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression

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Horticulture Research 2023年第11期10卷 82-95页

作者： Xin-Dong Xu Ru-Peng Zhao Liang Xiao Liuying Lu Min Gao Yu-Hong Luo Zu-Wen Zhou Si-Ying Ye Yong-Qing Qian Bing-Liang Fan Xiaohong Shang Pingli Shi Wendan Zeng Sheng Cao Zhengdan Wu Huabing Yan Ling-Ling Chen jia-ming song State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China Cash Crops Research Institute Guangxi Academy of Agricultural SciencesNanning 530007China

Cassava is a crucial crop that makes a significant contribution to ensuring human food ***,high-quality telomere-totelomere cassava genomes have not been available up to now,which has restricted the progress of haploid molecular breeding for *** this study,we constructed two nearly complete haploid resolved genomes and an integrated,telomere-to-telomere gap-free reference genome of an excellent cassava variety,‘Xinxuan 048’,thereby providing a new high-quality genomic ***,the evolutionary history of several species within the Euphorbiaceae family was *** comparative analysis of haploid genomes,it was found that two haploid genomes had extensive differences in linear structure,transcriptome features,and epigenetic *** located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis *** high heterozygosity of cassava‘Xinxuan 048’leads to rapid trait segregation in the first selfed *** study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.

关键词： breeding thereby evolution

High-quality genome assemblies for two Australimusa bananas(Musa spp.)and insights into regulatory mechanisms of superior fiber properties

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Plant Communications 2024年第1期5卷 245-261页

作者： Run Zhou Shuo Wang Ni Zhan Weidi He Guiming Deng Tongxin Dou Xi-Tong Zhu Wen-Zhao Xie Yu-Yu Zheng Chunhua Hu Fangcheng Bi Huijun Gao Tao Dong Siwen Liu Chunyu Li Qiaosong Yang Lingqiang Wang jia-ming song jiangbo Dang Qigao Guo Ganjun Yi Ling-Ling Chen Ou Sheng Institute of Fruit Tree Research Guangdong Academy of Agricultural SciencesKey Laboratory of South Subtropical Fruit Biology and Genetic Resource UtilizationMinistry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree ResearchGuangzhou 510640China College of Informatics Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China College of Horticulture and Landscape Architecture Southwest UniversityChongqing 400715China

Bananas(Musa spp.)are monocotyledonous plants with high genetic diversity in the Musaceae family that are cultivated mainly in tropical and subtropical *** fruits are a popular food,and the plants themselves have diverse *** genetic groups(genomes)are thought to have contributed to current banana cultivars:Musa acuminata(A genome),Musa balbisiana(B genome),Musa schizocarpa(S genome),and species of the Australimusa section(T genome).However,the T genome has not been effectively ***,we present the high-quality TT genomes of two representative accessions,Abaca(Musa textilis),with high-quality naturalfiber,and Utafun(Musa troglodytarum,Fe’i group),with abundant *** the Abaca and Utafun assemblies comprise 10 pseudochromosomes,and their total genome sizes are 613 Mb and 619 Mb,*** genome analysis revealed that the larger size of the T genome is likely attributable to rapid expansion and slow removal of *** with those of Musa AA or BB accessions or sisal(Agava sisalana),Abacafibers exhibit superior mechanical properties,mainly because of their thicker cell walls with a higher content of cellulose,lignin,and *** of MusaCesA cellulose synthesis genes peaks earlier in Abaca than in AA or BB accessions during plant development,potentially leading to earlier cellulose accumulation during secondary cell wall *** Abaca-specific expressed gene MusaMYB26,which is directly regulated by MusaMYB61,may be an important regulator that promotes precocious expression of secondary cell wall ***,MusaWRKY2 and MusaNAC68,which appear to be involved in regulating expression of MusaLAC and MusaCAD,may at least partially explain the high accumulation of lignin in *** work contributes to a better understanding of banana domestica-tion and the diverse genetic resources in the Musaceae family,thus providing resources for Musa genetic improvement.

关键词： Australimusa bananas T genome Musaceae evolution structural variations fiber

Passive activity enhances residual control ability in patients with complete spinal cord injury

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Neural Regeneration Research 2025年第8期20卷 2337-2347页

作者： Yanqing Xiao mingming Gao Zejia He jia Zheng Hongming Bai jia-Sheng Rao Guiyun song Wei song Xiaoguang Li Beijing Key Laboratory for Biomaterials and Neural Regeneration Beijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringBeihang UniversityBeijingChina Department of Rehabilitation Evaluation China Rehabilitation Research CenterBeijingChina Cardiac Center Beijing Children’s HospitalCapital Medical UniversityBeijingChina The State Key Laboratory of Virtual Reality Technology and Systems Beihang UniversityBeijingChina Department of Rehabilitation Engineering China Rehabilitation Science InstituteBeijingChina

Patients with complete spinal cord injury retain the potential for volitional muscle activity in muscles located below the spinal injury ***,because of prolonged inactivity,initial attempts to activate these muscles may not effectively engage any of the remaining neurons in the descending pathway.A previous study unexpectedly found that a brief clinical round of passive activity significantly increased volitional muscle activation,as measured by surface *** this study,we further explored the effect of passive activity on surface electromyographic signals during volitional control tasks among individuals with complete spinal cord *** patients with chronic complete thoracic spinal cord injury were *** electromyography data from eight major leg muscles were acquired and compared before and after the passive activity *** results indicated that the passive activity led to an increased number of activated volitional muscles and an increased frequency of *** the cumulative root mean square of surface electromyography amplitude for volitional control of movement showed a slight increase after passive activity,the difference was not statistically *** findings suggest that brief passive activity may enhance the ability to initiate volitional muscle activity during surface electromyography tasks and underscore the potential of passive activity for improving residual motor control among patients with motor complete spinal cord injury.

关键词： complete spinal cord injury cycle training epidural electrical stimulation motor training passive activity physiological state spinal cord circuit surface electromyography volitional control task

Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control

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Plant Communications 2024年第2期5卷 243-260页

作者： Wen-Zhao Xie Yu-Yu Zheng Weidi He Fangcheng Bi Yaoyao Li Tongxin Dou Run Zhou Yi-Xiong Guo Guiming Deng Wenhui Zhang Min-Hui Yuan Pablo Sanz-Jimenez Xi-Tong Zhu Xin-Dong Xu Zu-Wen Zhou Zhi-Wei Zhou jia-Wu Feng Siwen Liu Chunyu Li Qiaosong Yang Chunhua Hu Huijun Gao Tao Dong jiangbo Dang Qigao Guo Wenguo Cai jianwei Zhang Ganjun Yi jia-ming song Ou Sheng Ling-Ling Chen Institute of Fruit Tree Research Guangdong Academy of Agricultural SciencesKey Laboratory of South Subtropical Fruit Biology and Genetic Resource UtilizationMinistry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree ResearchGuangzhou 510640China College of Informatics Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China College of Horticulture and Landscape Architecture Southwest UniversityChongqing 400715China

Bananas(Musa spp.)are one of the world’s most important fruit crops and play a vital role in food security for many developing *** banana cultivars are triploids derived from inter-and intraspecific hybrid-izations between the wild diploid ancestor species Musa acuminate(AA)and ***(BB).We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types,Plantain and Silk,and precisely characterize ancestral contributions by examining ancestry mosaics across the *** asymmetric evolution is observed in their subgenomes,which can be linked to frequent homol-ogous exchange *** reveal the genetic makeup of triploid banana cultivars and verify that subge-nome B is a rich source of disease resistance *** 58.5%and 59.4%of Plantain and Silk genes,respectively,are present in all three haplotypes,with>50%of genes being differentially expressed alleles in different *** observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4(Foc TR4),which con-firms that Plantain can initiate defense responses faster than ***,we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and *** study provides resources for better understanding the genomic architecture of culti-vated bananas and has important implications for Musa genetics and breeding.

关键词： bananas Plantain Silk asymmetric evolution homologous exchange Fusarium wilt

Inhibiting SHP2 reduces glycolysis, promotes microglial M1 polarization, and alleviates secondary inflammation following spinal cord injury in a mouse model

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Neural Regeneration Research 2025年第3期20卷 858-872页

作者： Xintian Ding Chun Chen Heng Zhao Bin Dai Lei Ye Tao song Shuai Huang jia Wang Tao You Department of Orthopedics The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina Department of Orthopedics Provincial Hospital Affiliated to Anhui Medical UniversityHefeiAnhui ProvinceChina

Reducing the secondary inflammatory response, which is partly mediated by microglia, is a key focus in the treatment of spinal cord injury. Src homology 2-containing protein tyrosine phosphatase 2(SHP2), encoded by PTPN11, is widely expressed in the human body and plays a role in inflammation through various mechanisms. Therefore, SHP2 is considered a potential target for the treatment of inflammation-related diseases. However, its role in secondary inflammation after spinal cord injury remains unclear. In this study, SHP2 was found to be abundantly expressed in microglia at the site of spinal cord injury. Inhibition of SHP2 expression using siRNA and SHP2 inhibitors attenuated the microglial inflammatory response in an in vitro lipopolysaccharide-induced model of inflammation. Notably, after treatment with SHP2 inhibitors, mice with spinal cord injury exhibited significantly improved hind limb locomotor function and reduced residual urine volume in the bladder. Subsequent in vitro experiments showed that, in microglia stimulated with lipopolysaccharide, inhibiting SHP2 expression promoted M2 polarization and inhibited M1 polarization. Finally, a co-culture experiment was conducted to assess the effect of microglia treated with SHP2 inhibitors on neuronal cells. The results demonstrated that inflammatory factors produced by microglia promoted neuronal apoptosis, while inhibiting SHP2 expression mitigated these effects. Collectively, our findings suggest that SHP2 enhances secondary inflammation and neuronal damage subsequent to spinal cord injury by modulating microglial phenotype. Therefore, inhibiting SHP2 alleviates the inflammatory response in mice with spinal cord injury and promotes functional recovery postinjury.

关键词： apoptosis glycolysis inflammatory response microglia neurons polarization spinal cord injury Src homology 2-containing protein tyrosine phosphatase 2

Pan-transcriptomic analysis of rice under cold stress reveals alternative splicing control of cold tolerance

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Pan-transcriptomic analysis of rice under cold stress reveal...

第二十届中国作物学会学术年会

作者： Yuanyuan Zhong Yuhong Luo Jinliang Sun Xuemei Qin Ping Gan Zuwen Zhou Yongqing Qian Rupeng Zhao Zhiyuan Zhao Wenguo Cai Jijing Luo Ling-Ling Chen jia-ming song State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi University College of Informatics Huazhong Agricultural University

Plants have evolved sophisticated mechanisms to adapt to harsh environmental conditions, but cold stress response in rice, a staple food crop sensitive to low temperatures, remains poorly understood and thus a limiting factor for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterize the transcriptional regulatory landscape of rice in response to cold stress through Iso-Seq and RNASeq data of 11 rice cultivars subjected to a time course of cold treatment. Moreover, our analyses revealed that regulation of gene expression through alternative splicing plays a significant role in the cold stress response and identified OsCATC and Os03g0701200 as new candidate genes for engineering cold-tolerance enhancement. Importantly, we uncovered central roles in cold tolerance for two serine-arginine-rich splicing factors OsRS33 and OsRS2Z38, and our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a significant selection gene in the domestication process of Japonica rice for cold adaptation. This study systematically investigated the alternative splicing distribution, dynamic changes, and regulatory mechanisms of rice under cold stress to generate insights and a rich resource with broad implications for understanding the precise regulation of plants under cold stress and the genetic basis of cold response mechanisms.

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瞬时频谱分析法在海洋电磁信号分析中的应用

实验室研究与探索 2014年第3期33卷 4-7页

作者：周逢道周继瑜刘长胜贾明松吉林大学仪器科学与电气工程学院吉林长春130026 华能吉林发电有限公司吉林长春130000

海洋可控源电磁法(CSEM)是近年兴起的一种探测海底油气的地球物理技术。CSEM在深海取得了很好的效果,但是在浅海受空气波的影响严重,沿空气-海水分界面传播的空气波会完全掩盖从高阻储油层返回的有用信号。通过对时频分析技术的研究,达... 详细信息

海洋可控源电磁法(CSEM)是近年兴起的一种探测海底油气的地球物理技术。CSEM在深海取得了很好的效果,但是在浅海受空气波的影响严重,沿空气-海水分界面传播的空气波会完全掩盖从高阻储油层返回的有用信号。通过对时频分析技术的研究,达到对空气波的压制的目的。研究和对比短时傅里叶变换、WignerVille分布和希尔伯特-黄变换3种常用的时频分析方法,选取Wigner-Ville变换对海洋电磁信号进行时频分析,因为海洋电磁信号在空气和海底中传播速度的不同,所以接收点通过两种途径接收到的信号的时间也不同,通过理论计算进而判断出所需要的海底传播的信号,为压制空气波提供技术方法。

关键词：海洋可控源电磁法信号处理时频分析瞬时频谱