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Rosaceae phylogenomic studies provide insights into the evolution of new genes

Horticultural Plant Journal 2025年第1期11卷 389-405页

作者： Lan Jiang Xiaoxu Li Kun Lyu Han Wang Zhiyuan Li Wang Qi Lin Zhang Yunpeng Cao Anhui Province Key Laboratory of Non-coding RNA Basic and Clinical Transformation(Wannan Medical College) Central LaboratoryYijishan Hospital of Wannan Medical CollegeWuhuAnhui 241000China Beijing Life Science Academy Beijing 102209China CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhanHubei 430074China Center of Economic Botany Core Botanical GardensChinese Academy of SciencesWuhanHubei 430074China Key Laboratory for Tobacco Gene Resources Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoShangdong 266000China school of Life sciences Anhui Agricultural UniversityHefeiAnhui 230036China School of Basic Medical sciences Hubei University of Chinese MedicineWuhanHubei 430065China

Rosa banksiae,known as Lady Banks'rose,is a perennial ornamental crop and a versatile herb in traditional Chinese *** the lack of genomic resources,we assembled a Hi Fi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality *** genome with a scaffold N50=63.90 *** genome of *** exhibited no lineage-specific whole-genome duplication compared with other *** phylogenomic analysis of 13 Rosaceae and Arabidopsis through a comparative genomics study showed that numerous gene families were lineage-specific both before and after the diversification of *** of these genes are candidates for new genes that have evolved from parental genes through fusion *** genes are divided into three types:Type-I and Type-II genes contain two parental genes that are generated by duplication,distributed in the same and different regions of the genome,respectively;and Type-III can only be detected in one parental ***,Type-I genes are found to have more relaxed selection pressure and lower Ks values than Type-II,indicating that these newly evolved Type-I genes may play important roles in driving phenotypic *** analysis exhibited that newly formed fusion genes can regulate the phenotype traits of plant growth and development,suggesting the functional significance of these *** study identifies new fusion genes that could be responsible for phenotype evolution and provides information on the evolutionary history of recently diverged species in the Rosa *** data represents the major progress in understanding the new fusion genes evolution pattern of Rosaceae and provides an invaluable resource for phylogenomic studies in plants.

关键词： Rosa banksiae Gap-free genome Rosaceae Phenotype Evolutionary patterns

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Development and molecular cytogenetic identification of a new wheat-rye 6RL ditelosomic addition and 1R(1B)substitution line with powderymildew resistance

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Journal of Integrative Agriculture 2025年第1期24卷 72-84页

作者： Guohao Han Jing Wang Hanwen Yan Lijun Cao Shiyu Liu Xiuquan Li Yilin Zhou Wei Liu Tiantian Gu Zhipeng Shi Hong Liu Lihui Li Diaoguo An Center for Agricultural Resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050022China National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop sciences Chinese Academy of AgriculturalSciencesBeijing 100081China State Key Laboratory for Biology of Plant Disease and Insect Pests/Institute of Plant Protection Chinese Academy of Agricultural SciencesBeijing 100193China Innovation Academy of Seed Design Chinese Academy of SciencesBeijing 100101China

Powdery mildew is a serious disease caused by Blumeria graminis ***(Bgt)that critically threatens the yield and quality of wheat(Triticum aestivum L.).Using effective powdery mildew resistance genes is the optimal method for controlling this *** the background of high genetic homogeneity among the modern commercial cultivars that are mainly derived from conventional interbreeding,the resistance genes from wheat relatives have especially prominent *** triticale,produced from common wheat and rye(Secale cereale L.)through distant hybridization,is a new synthetic species and valuable gene donor for wheat *** this study,we developed the wheat-rye line YT5 through the hybridization of octaploid triticale and two wheat ***5 was confirmed to be a 6RL ditelosomic addition and 1R(1B)substitution line using genomic in situ hybridization(GISH),multicolor fluorescence in situ hybridization(mc-FISH),multicolor GISH(mc-GISH)and molecular marker *** analysis showed that the powdery mildew resistance in YT5 was derived from the rye chromosome arm *** inoculation with different Bgt isolates at the seedling stage,YT5 had compound reaction patterns with both obvious spores and hypersensitivity,and it gradually became highly resistant until the adult-plant stage,thus showing a resistance response significantly different from the reported Pm genes from rye chromosome ***5 also showed promising agronomic performance,so it is expected to be an elite resistance donor for wheat *** promote the transfer of the chromosome arm 6RL of YT5 in marker-assisted selection(MAS)breeding,we selected and verified two 6RL-specific kompetitive allelespecific PCR(KASP)markers that can be applied to efficiently detect this chromosome arm in different wheat backgrounds.

关键词： powdery mildew common wheat Triticale 6RL ditelosomic addition line agronomic performance marker-assisted selection(MAS)

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TPMGD:A genomic database for the traditional medicines in Pakistan

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Chinese Herbal Medicines 2025年第1期17卷 87-93页

作者： Rushuang Xiang Huihua Wan Wei Sun Baozhong Duan Weiqian Chen Xue Cao Sifan Wang Chi Song Shilin Chen Yan Wang Atia-tul Wahab M.Iqbal Choudhary Xiangxiao Meng State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences College of Pharmaceutical Science Dali University H.E.J.Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi Dr.Panjwani Center for Molecular Medicine and Drug Research International Center for Chemical and Biological Sciences University of Karachi

Objective:In Pakistan,traditional medicines are an important component of the medical system,with numerous varieties and great ***,due to the scattered resources and the lack of systematic collection and collation,adulteration of traditional Pakistani medicine(TPM) is common,which severely affects the safety of their medicinal use and the import and export ***,it is urgent to systematically organize and unify the management of TPM and establish a set of standards and operable methods for the identification of ***:We collected and organized the information on 128 TPMs with regard to their medicinal parts,efficacy,usage,and genetic material,based on Pakistan Hamdard Pharmacopoeia of Eastern Medicine:Pharmaceutical *** genetic information of TPM is summarized from national center for biotechnology information(NCBI) and global pharmacopoeia genome database(GPGD).Furthermore,we utilized bioinformatics technology to supplement the chloroplast genome(cp-genome) data of 12 *** build the web server,we used the Linux+Apache+MySQL+PHP(LAMP) system and constructed the webpage on a PHP:Hypertext Preprocessor(PHP) model view controller(MVC) ***:We constructed a new genomic database,the traditional Pakistani medicine genomic database(TPMGD).This database comprises five entries,namely homepage,medicinal species,species identification,basic local alignment search tool(BLAST),and ***,TPMGD contains basic profiles of 128 TPMs and genetic information of 102 TPMs,including 140 cytochrome c oxidase subunit I(COI)sequences and 119 mitochondrial genome sequences from Bombyx mori,1 396 internal transcribed spacer 2(ITS2) sequences and 1 074 intergenic region(psbA-trnH) sequences specific to 92 and 83 plant species,***,TPMGD includes 199 cp-genome sequences of 82 ***:TPMGD is a multifunctional database that integrates species description,functional information inquiry,genetic information

关键词： chloroplast genome database DNA barcodes Pakistan traditional medicine

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The priming induction regimen of HAG as a low dose chemotherapy strategy in AML clonal evolution

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Science China(Life sciences) 2015年第12期58卷 1302-1305页

作者： CHEN AiLi YANG JingYi HU ShaoYan WANG Qian-Fei Key Laboratory of genomic and Precision Medicine Beijing Institute of Genomics Chinese Academy of Sciences The Children's Hospital of Soochow University

Chemotherapy employs chemical substances to interfere with the growth of cancer cells,and is a major treatment strategy in human cancer including acute myeloid leukemia（AML）.Although they often effectively kill fast... 详细信息

关键词： regimen chemotherapy clonal interfere myeloid dividing subgroup induction clone relapse

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Whole-brain patterns of the presynaptic inputs and axonal projections of BDNF neurons in the paraventricular nucleus

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Journal of Genetics and genomics 2019年第1期46卷 31-40页

作者： Fang Luo Yuling Mu Cuicui Gao Yan Xiao Qian Zhou Yiqing Yang Xinyan Ni Wei L.Shen Jiajun Yang undergraduate program and School of Life Science and Technology ShanghaiTech University Institute of Neuroscience Shanghai Institutes for Biological Sciences Chinese Academy of Sciences University of Chinese Academy of sciences Department of Neurology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Department of Neurology Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Science

Brain-derived neurotrophic factor (BDNF) plays a crucial role in human obesity. Yet, the neural circuitry supporting the BDNF-mediated control of energy homeostasis remains largely undefined. To map key regions that might provide inputs to or receive inputs from the paraventricular nucleus (PVN) BDNF neurons, a key type of cells in regulating feeding and thermogenesis, we used rabies virus-based transsynaptic labeling and adeno-associated virus based anterograde tracing techniques to reveal their whole-brain distributions. We found that dozens of brain regions provide dense inputs to or receive dense inputs from PVN BDNF neurons, including several known weight control regions and several novel regions that might be functionally important for the BDNF-mediated regulation of energy ***, several regions show very dense reciprocal connections with PVN BDNF neurons, including the lateral septum, the preoptic area, the ventromedial hypothalamic nucleus, the paraventricular thalamic nucleus, the zona incerta, the lateral parabrachial nucleus, the subiculum, the raphe magnus nucleus, and the raphe pallidus nucleus. These strong anatomical connections might be indicative of important functional connections. Therefore, we provide an outline of potential neural circuitry mediated by PVN BDNF neurons, which might be helpful to resolve the complex obesity network.

关键词： BDNF Transsynaptic tracing Obesity Feeding Thermogenesis

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Application of liquid biopsy in precision medicine： opportunities and challenges

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Frontiers of Medicine 2017年第4期11卷 522-527页

作者： Junyun Wang Shuang Chang Guochao Li Yingli Sun Key Laboratory of genomic and Precision Medicine China Gastrointestinal Cancer Research CenterBeijing Institute of GenomicsChineseAcademy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China

Precision medicine for cancer patients aims to adopt the most suitable treatment options during diagnosis and treatment of individuals. Detecting circulating tumor cell （CTC） or circulating tumor DNA （ctDNA） in plasma or serum could serve as liquid biopsy, which would be useful for numerous diagnostic applications. Liquid biopsies can help clinicians screen and detect cancer early, stratify patients to the most suitable treatment and real-time monitoring of treatment response and resistance mechanisms in the tumor, evaluate the risk for metastatic relapse, and estimate prognosis. We summarized the advantages and disadvantages of tissue and liquid biopsies. We also further compared and analyzed the advantages and limitations of detecting CTCs, ctDNAs, and exosomes. Furthermore, we reviewed the literature related with the application of serum or plasma CTCs, ctDNAs, and exosomes for diagnosis and prognosis of cancer. We also analyzed their opportunities and challenges as future biomarkers. In the future, liquid biopsies could be used to guide cancer treatment. They could also provide the ideal scheme to personalize treatment in precision medicine.

关键词： liquid biopsy circulating tumor cells cell-free ctDNA exosomes precision medicine

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Genetic diversity of the self-incompatibility locus in diploid potato

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Journal of Integrative Agriculture 2025年第04期 1448-1460页

作者： Xinyu Jing Duoduo Qian Xiuhan Jiang Pei Wang Huihui Bao Dianjue Li Yanhui Zhu Guangtao Zhu Chunzhi Zhang National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture/Key Laboratory of Synthetic Biology Ministry of Agriculture and Rural Affairs/Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences State Key Laboratory of Crop Stress Adaptation and Improvement School of Life Sciences Henan University Yunnan Key Laboratory of Potato Biology The AGISCAAS–YNNU Joint Academy of Potato Sciences Yunnan Normal University

Re-domestication of diploid potato (Solanum tuberosum) into a seed crop is an innovative breeding method to accelerate genetic *** propagation would allow hybrid production and mix superior ***, almost all diploid potatoes in nature are self-incompatible (SI).Gametophytic self-incompatible (GSI) is a widespread SI in Solanaceae and is controlled by the S locus that contains a ribonuclease (S-RNase) and multiple F-box (SLFs); however, the genetic diversity of the S locus in potato is *** study identified 21 S-RNase alleles involved in SI from 194 diploid potato accessions by large-scale transcriptome *** levels of amino acid similarity among different S-RNase proteins varied from 31.3 to 95.8%.S2 allele is the most widespread in 194 diploid potatoes and is mainly distributed in the S. tuberosum Group *** on genomic annotation and expression analysis, we identified 12 potential functional SI male-determinant genes, S-locus F-box (SLFs),encoding F-box proteins in the S2 locus on a genomic region of approximately 13 *** genomics analysis showed that eight SLF genes are relatively conserved among four homozygous S *** Ka and Ks analysis suggested that S-RNase and intra-haplotypic SLF genes have *** findings help select suitable pollinators, combine more hybrid combinations, and fully use heterosis to accelerate diploid potato breeding.

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DNA methylation signatures in circulating cell-free DNA as biomarkers for the early detection of cancer

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Science China(Life sciences) 2017年第4期60卷 356-362页

作者： Junyun Wang Xiao Han Yingli Sun Key Laboratory of genomic and Precision Medicine China Gastrointestinal Cancer Research Center Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of sciences Beijing 100049 China

Detecting cell-free DNA(cfDNA) or circulating tumor DNA(ctDNA) in plasma or serum could serve as a "liquid biopsy", which would be useful for numerous diagnostic applications. cfDNA methylation detection is one of the most promising approaches for cancer risk assessment. Here, we reviewed the literature related to the use of serum or plasma circulating cell-free DNA for cancer diagnosis in the early stage and their power as future biomarkers.

关键词： methylation circulating DNA alterations biopsy numerous diagnostic metastatic screening colorectal

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genomic insights into demographic history,structural variation landscape,and complex traits from 514 Hu sheep genomes

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Journal of Genetics and genomics 2025年第2期52卷 245-257页

作者： Kaiyu Chen Yuelang Zhang Yizhe Pan Xin Xiang Chen Peng Jiayi He Guiqing Huang Zhengguang Wang Pengju Zhao College of Animal sciences Zhejiang UniversityHangzhouZhejiang 310058China Hainan Institute Zhejiang UniversitySanyaHainan 572000China Agricultural Product Quality and Safety Research Center of Huzhou City HuzhouZhejiang 313000China

Hu sheep is an indigenous breed from the Taihu Lake Plain in China,known for its high *** Hu sheep belong to the Mongolian group,their demographic history and genetic architecture remain ***,we analyze 697 sheep genomes from representatives of Mongolian sheep *** study suggests that the ancestral Hu sheep first separated from the Mongolian group approximately 3000 years *** Hu sheep migrated from the north and flourished in the Taihu Lake Plain around 1000 years ago,they developed a unique genetic foundation and phenotypic characteristics,which are evident in the genomic footprints of selective sweeps and structural variation *** associated with reproductive traits(BMPR1B and TDRD10)and horn phenotype(RXFP2)exhibit notable selective sweeps in the genome of Hu sheep.A genome-wide association analysis reveals that structural variations at LOC101110773,MAST2,and ZNF385B may significantly impact polledness,teat number,and early growth in Hu sheep,*** study offers insights into the evolutionary history of Hu sheep and may serve as a valuable genetic resource to enhance the understanding of complex traits in Hu sheep.

关键词： Hu sheep Population sequencing Demographic history Structural variation Genome-wide association study

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Aberrant Somatic Hypermutation at Super-enhancer Drives B Cell Lymphoma Transformation

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genomics, Proteomics & Bioinformatics 2024年第4期22卷 191-193页

作者： Xueshuai Han Zhaoqi Liu CAS Key Laboratory of genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of sciences Beijing 100049China

Background Most B cell lymphomas can be traced back to the germinal center(GC)or B cells that have undergone GC *** the GC,B cells undergo somatic hypermutation(SHM)and class switch recombination,generating memory B cells or plasma cells with high-affinity antibodies against *** studies suggest that the occurrence of activationinduced deaminase(AID)-mediated SHM processes outside the immunoglobulin gene loci may promote the development of *** pathological off-targeting of SHM is termed aberrant SHM(aSHM).The DNA targets and potential functional consequences of aSHM are still largely ***,through the whole-genome sequencing analysis of longitudinally paired samples representing the transformation from follicular lymphoma(FL)to double-hit lymphoma(DHL,with MYC and BCL2 rearrangements),Uttiya Basu and Jiguang Wang labs have found that the majority of aSHM is distributed around promoter regions embedded within super-enhancers(SEs)[1].They also reveal that aSHM within SEs can affect the transcription of neighboring genes through enhancer retargeting.

关键词： Transformation consequences representing

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