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Horticultural Plant Journal 2023年第4期9卷 693-704页

作者： Chenyang Han Huizhen Dong Qinghai Qiao Yuqin Dai Xiaosan Huang Shaoling Zhang College of Horticulture State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingJiangsu 210095China

N 6-methylated adenine(m6 A)is an emerging epigenetic marker in eukaryotic organisms that plays an important role in biological functions and in enriching genetic information.m6 A exerts these functions via the dynamic interplay among m6 A writers,erasers,and ***,little is known about the underlying mechanisms of m6 A in plant growth and stress ***,we identified 276 masked m6 A regulators from nine Rosaceae species(Pyrus bretschneideri,Pyrus betulifolia,Pyrus communis,Malus domestica,Fragaria vesca,Prunus avium,Prunus mume,Prunus persica,and Rubus occidentalis).We classified and named these genes in more detail based on phylogenetic and synteny *** expansion of m6 A regulators in Maloideae was dated back to the recent whole-genome duplication(WGD)in *** on the expression pattern analysis and gene structure analysis of m6 A regulators,m6 A was shown to be a significant factor in regulating plant development and *** addition,PbrMTA1-silenced pear plants displayed significantly reduced drought tolerance and chlorophyll content,as well as increased electrolyte leakage and concentrations of malondialdehyde and H2 O2.

关键词： Pyrus bretschneideri RNA methylation m6A regulators Rosaceae Evolution Transcriptome Drought stress VIGS

Nuclear phylogeny and insights into wholegenome duplications and reproductive development of Solanaceae plants

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Plant Communications 2023年第4期4卷 301-322页

作者： Jie Huang Weibin Xu Junwen Zhai Yi Hu Jing Guo Caifei Zhang Yiyong Zhao Lin Zhang Christopher Martine Hong Ma Chien-Hsun Huang State key laboratory of Genetic Engineering and Collaborative Innovation Center of genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200438China Guangxi key laboratory of Plant Conservation and Restoration Ecology in Karst Terrain Guangxi Institute of BotanyGuangxi Zhuangzu Autonomous Region and Chinese Academy of SciencesGuilin 541006China key laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of biology the Huck Institutes of Life Sciencesthe Pennsylvania State UniversityUniversity ParkState CollegePA 16802USA Department of biology Bucknell UniversityLewisburgPA 17837USA

Solanaceae,the nightshade family,have2700 species,including the important crops potato and tomato,ornamentals,and medicinal *** sequenced Solanaceae genomes show evidence for wholegenome duplication(WGD),providing an excellent opportunity to investigate WGD and its ***,we generated 93 transcriptomes/genomes and combined them with 87 public datasets,for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 *** 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major *** Solanaceae tree supports four previously recognized subfamilies(Goetzeioideae,Cestroideae,Nicotianoideae,and Solanoideae)and the designation of three other subfamilies(Schizanthoideae,Schwenckioideae,and Petunioideae),with the placement of several previously unassigned *** placed a Solanaceae-specific whole-genome triplication(WGT1)at81 million years ago(mya),before the divergence of Schizanthoideae from other Solanaceae subfamilies at73 *** addition,we detected two gene duplication bursts(GDBs)supporting proposed WGD events and four other *** investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene(sub)families revealed that 21 gene clades have retained gene *** were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit *** study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development,providing an improved understanding of Solanaceae evolution.

关键词： Solanaceae phylogeny transcriptome carpel and fruit development whole-genome duplication

Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum

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Journal of Integrative Agriculture 2022年第11期21卷 3230-3244页

作者： LIU Lei WANG Heng-bo LI Yi-han CHEN Shu-qi WU Ming-xing DOU Mei-jie QI Yi-yin FANG Jing-ping ZHANG Ji-sen Center for genomics and Biotechnology Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsFujian Agriculture and Forestry UniversityFuzhouFujian 350002P.R.China State key Lab for Conservation and Utilization of Subtropical Agro-Biological Resources&Guangxi key Lab for Sugarcane biology Guangxi UniversityNanning 530004P.R.China College of Life Sciences Fujian Normal UniversityFuzhou 350007P.R.China

Sugarcane has a large,complex,polyploid genome that has hindered the progress of genomic research and molecular marker-assisted *** user-friendly SSR markers have attracted considerable attention owing to their ideal genetic ***,these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane *** this present study,744305and 361638 candidate SSRs were identified from the genomes of *** and ***,*** verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum,including ***,***,***,and modern sugarcane *** results showed that 660 SSR markers displayed interspecific polymorphisms among these ***,100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions.A total of 320 alleles were generated using 100 polymorphic primers,with each marker ranging from two to seven *** genetic diversity analysis revealed that these accessions were distributed in four main groups,including group I(14 *** accessions),group II(two *** accessions),group III(18 modern sugarcane hybrid accessions),and group IV(five *** accessions).Experimental verification supported the reliability of the SSR markers based on genome-wide *** development of a large number of SSR markers based on wet experiments is valuable for genetic studies,including genetic linkage maps,comparative genome analysis,genome-wide association studies,and marker-assisted selection in Saccharum.

关键词： Saccharum genome-wide simple repeat sequences(SSR) microsatellite molecular markers

Cloning and characterization of a novel member of human β-1, 4-galactosyltransferase gene family

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Science China(Life Sciences) 1999年第4期42卷 337-345页

作者：范玉新余龙张琪江萤戴方彦陈驰原屠强毕安定许月芳赵寿元 1. State key laboratory of Genetic Engineering Institute of Genetics Fudan University 200433 Shanghai China

By using the EST strategy for identifying novel members belonging to homologous gene families, a novel full-length cDNA encoding a protein significantly homologous to UDP-Gal: N-acetylglucosamine β-1, 4-galactosyl-transferase (GalT) was isolated from a human testis cDNA library. A nucleotide sequence of 2 173 bp long was determined to contain an open reading frame of 1 032 nucleotides (344 amino acids) . In view of the homology to members of the galactosyltransferase gene family and especially the closest relationship to Gallus gallus GalT type I (CK I) , the predicted product of the novel cDNA was designated as human β-1,4-galactosyltransferase homolog I (HumGT-Hl) . Its mRNA is present in different degrees in 16 tissues examined. Southern analysis of human genomic DNA revealed its locus on chromosome 3 .

关键词： β-1 4-galactosyltransferase cDNA homolog.

Dissecting the key genomic regions underlying high yield potential in common wheat variety‘Kenong 9204’

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Journal of Integrative Agriculture 2023年第9期22卷 2603-2616页

作者： ZHAO Chun-hua ZHANG Na FAN Xiao-li JI Jun SHI Xiao-li CUI Fa LING Hong-qing LI Jun-ming College of Agriculture Ludong University/Key Laboratory of Molecular Module-based Breeding of High Yield and Abiotic Resistant Plants in Universities of ShandongYantai 264025P.R.China Jiangsu Xuhuai Regional Institute of Agricultural Sciences Xuzhou 221131P.R.China Chengdu Institute of biology Chinese Academy of SciencesChengdu 610041P.R.China State key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijng 100101P.R.China Center for Agricultural Resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050022P.R.China key laboratory of Molecular and Cellular biology Ministry of Education/Hebei Collaboration Innovation Center for Cell Signaling/Hebei Key Laboratory of Molecular and Cellular Biology/College of Life SciencesHebei Normal UniversityShijiazhuang 050024P.R.China

The foundation parents play key roles in the genetic improvement of both yield potential and end-use quality in *** the genetic basis that underlies certain beneficial traits in the foundation parents will provide theoretical reference for molecular breeding by a design approach.‘Kenong 9204’(KN9204)is a candidate foundation parent characterized by ideotype,high yield potential,and particularly high nitrogen fertilizer *** better understand the genetic basis of its high yield potential,high throughput whole-genome re-sequencing(10×)was performed on KN9204,its parental lines and its derivatives.A high-resolution genetic composition map of KN9204 was constructed,which showed the parental origin of the favorable genomic segments based on the identification of excellent yield-related quantitative trait loci(QTL)from a bi-parental mapping *** 693(XY693),a wheat–Thinopyrum ponticum partial amphidiploid,contributed a great deal to the high yield potential of KN9204,and three major stable QTLs from XY693 were fine *** transmissibility of key genomic segments from KN9204 to its derivatives were delineated,indicating that haplotype blocks containing beneficial gene combinations were conserved along with directional selection by *** for selection sweeps in the breeding programs was *** study provides a theoretical reference for the breeding of high-yield wheat varieties by a molecular design approach.

关键词： Kenong 9204 high-yielding potential quantitative trait locus genetic composition map key genomic regions

Super graph-based pan-genome: Bringing rice functional genomic study into a new dawn

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Molecular Plant 2022年第9期15卷 1409-1411页

作者： Yucheng Liu Zhixi Tian State key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100039China

Rice is one of the earliest domesticated crops that has been cultivated for thousands of ***,unlike other crops that are predominantly domesticated by a singleto neventin one place,the domestication of rice is quite complicated;it independently occurred in Asia and Africa toform the Asian cultivated rice Oryza sativa and the African cultivated rice ***,*** was mainly domesticated from the Asian wild rice *** in East/South Asia(Huang et al.,2012).Furthermore,*** can be classified into two main types:Geng(*** ***)and Xian(*** ***).Geng was domesticated as early as 9000 years ago,while Xian was domesticated lateralong with continuousgene flow from Geng(Choi etal.,2017).*** domesticated from African wild rice *** approximately 3500 years *** and *** diverged approximately 600000 years ago.

关键词： cultivated crops japonica

Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean

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Journal of genetics and genomics 2024年第4期51卷 379-393页

作者： Chao Fang Haiping Du Lingshuang Wang Baohui Liu Fanjiang Kong Guangdong key laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouGuangdong 510006China

Soybean(Glycine max[L.]Merr.)is an important crop that provides protein and vegetable oil for human *** soybean is a photoperiod-sensitive crop,its cultivation and yield are limited by the photoperiodic conditions in the *** contrast to other major crops,soybean has a special plant architecture and a special symbiotic nitrogen fixation system,representing two unique breeding ***,flowering time,plant architecture,and symbiotic nitrogen fixation are three critical or unique yielddetermining *** review summarizes the progress made in our understanding of these three critical yield-determining factors in ***,we propose potential research directions to increase soybean production,discuss the application of genomics and genomic-assisted breeding,and explore research directions to address future challenges,particularly those posed by global climate changes.

关键词： Soybean Grain yield Flowering time Plant architecture Nodulation Symbiotic nitrogen fixation Genome study

Water lilies as emerging models for Darwin’s abominable mystery

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Horticulture Research 2017年第1期4卷 105-111页

作者： Fei Chen Xing Liu Cuiwei Yu Yuchu Chen Haibao Tang Liangsheng Zhang Center for genomics and Biotechnology State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Ministry of Education for GeneticsBreeding and Multiple Utilization of CropsFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou350002China Zhejiang Humanities Landscape Co. LTDHangzhou310030China

Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering *** birth and rapid radiation of flowering plants has interested many scientists and was considered‘an abominable mystery’by Charles *** searching for the angiosperm evolutionary origin and its underlying mechanisms,the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages;however,little is known regarding the genetics and genomics of another basal angiosperm lineage,namely,the water *** this study,we reviewed current molecular research and note that water lily research has entered the genomic *** propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin’s‘abominable mystery’.Four pantropical water lilies,especially the recently sequenced Nymphaea colorata,have characteristics such as small size,rapid growth rate and numerous seeds and can act as the best model for understanding the origin of *** water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.

关键词： breeding origin occupy

Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process

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The Innovation 2021年第4期2卷 43-55页

作者： Ke-Jia Shan Changshuo Wei Yu Wang Qing Huan Wenfeng Qian State key laboratory of Plant genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in *** the molecular spectrum of de novo mutations—the relative rates at which various base substitutions occur—are widely recognized as informative toward understanding the evolution of a viral genome,little attention has been paid to the possibility of using molecular spectra to infer the host origins of a ***,we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines,enabled by the use of sporadic junctions formed during discontinuous transcription as molecular *** find that de novo mutations are generated in a replication-independent manner,typically on the genomic strand,and highly dependent on mutagenic mechanisms specific to the host cellular *** novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution,in an asymmetric manner favoring specific mutation ***,similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13,which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into ***,our findings provide data-driven support for the natural origin of SARS-CoV-2.

关键词： SARS-CoV-2 molecular spectrum de novo mutations mutational signature evolutionary origin mRNA mutation

Tumor initiation and early tumorigenesis:molecular mechanisms and interventional targets

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Signal Transduction and Targeted Therapy 2024年第7期9卷 2900-2935页

作者： Shaosen Zhang Xinyi Xiao Yonglin Yi Xinyu Wang Lingxuan Zhu Yanrong Shen Dongxin Lin Chen Wu Department of Etiology and Carcinogenesis National Cancer Center/National Clinical Research Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical College100021 BeijingChina key laboratory of Cancer genomic biology Chinese Academy of Medical Sciences and Peking Union Medical College100021 BeijingChina Changping laboratory 100021 BeijingChina Collaborative Innovation Center for Cancer Personalized Medicine Nanjing Medical UniversityNanjing 211166China Sun Yat-sen University Cancer Center State Key Laboratory of Oncology in South ChinaGuangzhou 510060China cams Oxford Institute Chinese Academy of Medical Sciences100006 BeijingChina

Tumorigenesis is a multistep process,with oncogenic mutations in a normal cell conferring clonal advantage as the initial ***,despite pervasive somatic mutations and clonal expansion in normal tissues,their transformation into cancer remains a rare event,indicating the presence of additional driver events for progression to an irreversible,highly heterogeneous,and invasive ***,researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution,independently of inducing ***,clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into ***,the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully *** this review,we summarize the genetic,epigenetic,and external driver events,and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution.A deeper understanding of the earliest molecular events holds promise for translational applications,predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.

关键词： alterations mechanisms restrain