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Telomere-to-telomere Genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subGenome divergence and mechanisms of alkaline stress tolerance

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Science China(Life Sciences) 2024年第1期67卷 149-160页

作者： Haofei Luo Xiaofei Wang Changqing You Xuedan Wu Duofeng Pan Zhiyao Lv Tong Li Dongmei Zhang Zhongbao Shen Xiaodong Zhang Guodao Liu Kaixuan He Qingtong Ye Yajun Jia Qinghua Zhao Xian Deng Xiaofeng Cao Xianwei Song Gai Huang State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Hainan Yazhou Bay Seed Lab Sanya 572025China University of Chinese Academy of Sciences Beijing 100049China Institute of Forage and Grassland Sciences Heilongjiang Academy of Agricultural SciencesHarbin 150086China Shandong Academy of Agricultural Sciences Jinan 250100China National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land Dongying 257345China Shandong Green Manure Ecological Technology Co. LtdDongying 257345China State Key Laboratory of Tropical Crop Breeding Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline soil.To understand Genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere Genome assembly of S.cannabina spanning~2,087 Mb.The assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric characteristics.Further Genome analysis distinguished A and B subGenomes,which diverged approximately 7.9 million years ago.Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A homoeolog.We further identified four specific alkali-induced phosphate transporter genes in S.cannabina;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil.Our work highlights the significance of S.cannabina as a green tool to improve marginal lands and sheds light on subGenome evolution and adaptation to alkaline soils.

关键词： Sesbania cannabina alkaline stress telomere-to-telomere Genome legume green manure phosphate transporter allotetraploid

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The Jasmine(Jasminum sambac)Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 127-149页

作者： Gang Chen Salma Mostafa Zhaogeng Lu Ran Du Jiawen Cui Yun Wang Qinggang Liao Jinkai Lu Xinyu Mao Bang Chang Quan Gan Li Wang Zhichao Jia Xiulian Yang Yingfang Zhu Jianbin Yan Biao Jin College of Horticulture and Plant Protection Yangzhou UniversityYangzhou 225009China College of Bioscience and Biotechnology Yangzhou UniversityYangzhou 225009China Department of Floriculture Faculty of AgricultureAlexandria UniversityAlexandria 21526Egypt Key Laboratory of Plant Functional Genomics of the Ministry of Education Yangzhou UniversityYangzhou 225009China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China College of Landscape Architecture Nanjing Forestry UniversityNanjing 210037China Institute of Plant Stress Biology State Key Laboratory of Cotton BiologyDepartment of BiologyHenan UniversityKaifeng 475001China

Jasminum sambac(jasmine flower),a world-renowned plant appreciated for its exceptional flower fragrance,is of cultural and economic importance.However,the genetic basis of its fragrance is largely unknown.Here,we present the first de novo Genome assembly of J.sambac with 550.12 Mb(scaffold N50=40.10 Mb)assembled into 13 pseudochromosomes.Terpene synthase(TPS)genes associated with flower fragrance are considerably amplified in the form of gene clusters through tandem duplications in the Genome.Gene clusters within the salicylic acid/benzoic acid/theobromine(SABATH)and benzylalcohol O-acetyltransferase/anthocyanin O-hydroxycinnamoyltransferases/anthranilate N-hydroxycinnamoyl/benzoyltransferase/deacetylvindoline 4-O-acetyltransferase(BAHD)superfamilies were identified to be related to the biosynthesis of phenylpropanoid/benzenoid compounds.Several key genes involved in jasmonate biosynthesis were duplicated,causing an increase in copy numbers.In addition,multi-omics analyses identified various aromatic compounds and many genes involved in fragrance biosynthesis pathways.Furthermore,the roles of JsTPS3 in b-ocimene biosynthesis,as well as JsAOC1 and JsAOS in jasmonic acid biosynthesis,were functionally validated.The Genome assembled in this study for J.sambac offers a basic genetic resource for studying floral scent and jasmonate biosynthesis,and provides a foundation for functional genomic research and variety improvements in Jasminum.

关键词： Jasmine flower Jasminum sambac Genome Jasmonate Flower fragrance

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Two haplotype-resolved,gap-free Genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit

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Molecular Plant 2023年第2期16卷 452-470页

作者： Xue Han Yilin Zhang Qiong Zhang Ni Ma Xiaoying Liu Wenjing Tao Zhiying Lou Caihong Zhong Xing Wang Deng Dawei Li Hang He Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in WeifangShandong 261325China School of Advanced Agricultural Sciences and School of Life Sciences Peking UniversityBeijing 100871China Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenThe Chinese Academy of SciencesWuhanHubei 430074China State Key Laboratory of Cellular Stress Biology School of Life SciencesFaculty of Medicine and Life SciencesXiamen UniversityXiamen 361102China

Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value,especially because of the high content of vitamin C in its fruit.In this study,we de novo assembled two telomere-to-telomere kiwifruit Genomes from Actinidia chinensis var.‘Donghong’(DH)and Actinidia latifolia‘Kuoye’(KY),with total lengths of 608327852 and 640561626 bp for 29 chromosomes,respectively.With a burst of structural variants involving inversion,translocations,and duplications within 8.39 million years,the metabolite content of DH and KY exhibited differences in saccharides,lignans,and vitamins.A regulatory ERF098 transcription factor family has expanded in KY and Actinidia eriantha,both of which have ultra-high vitamin C content.With each assembly phased into two complete haplotypes,we identified allelic variations between two sets of haplotypes,leading to protein sequence variations in 26494 and 27773 gene loci and allele-specific expression of 4687 and 12238 homozygous gene pairs.Synchronized metabolome and transcriptome changes during DH fruit development revealed the same dynamic patterns in expression levels and metabolite contents;free fatty acids and flavonols accumulated in the early stages,but sugar substances and amino acids accumulated in the late stages.The AcSWEET9b gene that exhibits allelic dominance was further identified to positively correlate with high sucrose content in fruit.Compared with wild varieties and other Actinidia species,AcSWEET9b promoters were selected in red-flesh kiwifruits that have increased fruit sucrose content,providing a possible explanation on why red-flesh kiwifruits are sweeter.Collectively,these two gap-free kiwifruit Genomes provide a valuable genetic resource for investigating domestication mechanisms and Genome-based breeding of kiwifruit.

关键词： kiwifruit Genome telomere-to-telomere allele-specific expression vitamin C sugar metabolism

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The Larix kaempferi Genome reveals new insights into wood properties

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Journal of Integrative Plant Biology 2022年第7期64卷 1364-1373页

作者： Chao Sun Yun-Hui Xie Zhen Li Yan-Jing Liu Xiao-Mei Sun Jing-Jing Li Wei-Peng Quan Qing-Yin Zeng Yves Van de Peer Shou-Gong Zhang State Key Laboratory of Tree Genetics and Breeding Chinese Academy of ForestryBeijing 100091China Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration Research Institute of ForestryChinese Academy of ForestryBeijing 100091China Department of Plant Biotechnology and Bioinformatics Ghent UniversityGent B‐9052Belgium VIB Center for Plant Systems Biology Ghent B‐9052Belgium Nextomics Biosciences Co. LtdWuhan 430073China Department of Biochemistry Genetics and MicrobiologyPretoriaSouth Africa

Here,through single-molecule real-time sequencing,we present a high-quality Genome sequence of the Japanese larch(Larix kaempferi),a conifer species with great value for wood production and ecological afforestation.The assembled Genome is 10.97 Gb in size,harboring 45,828 protein-coding genes.Of the Genome,66.8%consists of repeat sequences,of which long terminal repeat retrotransposons are dominant and make up 69.86%.We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses,unveiling their crucial roles in adaptive evolution.Population transcriptome analysis reveals that lignin content in L.kaempferi is mainly determined by the process of monolignol polymerization.The expression values of six genes(LkC OMT7,LkC OMT8,LkL AC23,LkL AC102,LkP RX148,and LkP RX166)have significantly positive correlations with lignin content.These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches’wood.Overall,this study provides new Genome resources for investigating the evolution and biological function of conifer trees,and also offers new insights into wood properties of larches.

关键词： evolution gene expression Genome Larix kaempferi wood properties

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Rising from the dead: the power of Genome editing

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Science China(Life Sciences) 2023年第12期66卷 2949-2951页

作者： Hongyuan Zheng Junyao Zhao Daowen Wang Zheng Qing Fu State Key Laboratory of Wheat and Maize Crop Science College of Agronomyand Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhou 450002China Department of Biological Sciences University of South CarolinaColumbia SC 29208USA

To protect themselves against diverse pathogens, plants have developed sophisticated defense mechanisms. Hypersensitive response or the rapid localized death of plant cells is a major defense strategy deployed by plan... 详细信息

关键词： dead Genome

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The Genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution

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Molecular Plant 2022年第6期15卷 1024-1044页

作者： Fang Yuan Xi Wang Boqing Zhao Xiaojing Xu Miao Shi Bingying Leng Xinxiu Dong Chaoxia Lu Zhongtao Feng Jianrong Guo Guoliang Han Haikuan Zhang Jianwei Huang Min Chen Bao-Shan Wang Shandong Provincial Key Laboratory of Plant Stress College of Life SciencesShandong Normal UniversityJi’nanShandongChina Berry Genomics Corporation BeijingChina

Halophytes have evolved specialized strategies to cope with high salinity.The extreme halophyte sea lavender(Limonium bicolor)lacks trichomes but possesses salt glands on its epidermis that can excrete harmful ions,such as sodium,to avoid salt damage.Here,we report a high-quality,2.92-Gb,chromosome-scale L.bicolor Genome assembly based on a combination of Illumina short reads,single-molecule,real-time long reads,chromosome conformation capture(Hi-C)data,and Bionano Genome maps,greatly enriching the genomic information on recretohalophytes with multicellular salt glands.Although the L.bicolor Genome contains genes that show similarity to trichome fate genes from Arabidopsis thaliana,it lacks homologs of the decision fate genes GLABRA3,ENHANCER OF GLABRA3,GLABRA2,TRANSPARENT TESTA GLABRA2,and SIAMESE,providing a molecular explanation for the absence of trichomes in this species.We identified key genes(LbHLH and LbTTG1)controlling salt gland development among classical trichome homologous genes and confirmed their roles by showing that their mutations markedly disrupted salt gland initiation,salt secretion,and salt tolerance,thus offering genetic support for the long-standing hypothesis that salt glands and trichomes may share a common origin.In addition,a whole-Genome duplication event occurred in the L.bicolor Genome after its divergence from Tartary buckwheat and may have contributed to its adaptation to high salinity.The L.bicolor Genome resource and genetic evidence reported in this study provide profound insights into plant salt tolerance mechanisms that may facilitate the engineering of salt-tolerant crops.

关键词： development evolution Genome Limonium bicolor salinity adaptation salt gland

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En Route to Completion:What Is An Ideal Reference Genome?

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 1-3页

作者： Weihua Pan Jue Ruan Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Since the Human Genome Project assembled the first draft human Genome 20 years ago[1],immense manpower,material,and financial resources have been cast for generating accurate,continuous,complete,and informative reference Genome for each important species.Nowadays,although the qualities of these Genome assemblies have been significantly improved compared to their initial draft versions.

关键词： species. Genome Genome

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A chromosome-level Genome assembly for Chinese plum‘Wushancuili'reveals the molecular basis of its fruit color and susceptibility to rain-cracking

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Horticultural Plant Journal 2024年第3期10卷 672-688页

作者： Kun Zhou Jingwen Wang Lin Pan Fang Xiang Yi Zhou Wei Xiong Ming Zeng Donald Grierson Wenbin Kong Lingyu Hu Wanpeng Xi College of Horticulture and Landscape Architecture Southwest UniversityChongqing 400715China Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River(Ministry of Education) Southwest UniversityChongqing 400715China Department of Pomology Chongqing Agricultural Technology Extension StationChongqing 401420China Plant and Crop Sciences Division School of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough LE125RDUK Wuxi Economical Crop Technology Extension Station Chongqing 405800China

Chinese plum(Prunus salicina Lindl.)originates from China and makes a large contribution to the global production of plums.The P.salicina‘Wushancuili'has a green coloration and high fruit quality and is economically important in eliminating poverty and protecting ecology in the Yangtze River Three Gorges Reservoir.However,rain-induced cracking(rain-cracking,literally skin cracking caused by rain)is a limitation to‘Wushancuili'fruit production and causes severe losses.This study reported a high-quality‘Wushancuili'Genome assembly consisting of a 302.17-Mb sequence with eight pseudo-chromosomes and a contig N50 of 23.59 Mb through the combination of Illumina sequencing,Pacific Biosciences HiFiⅢsequencing,and high-throughput chromosome conformation capture technology.A total of 25109 protein-coding genes are predicted and 54.17%of the Genome is composed of repetitive sequences.‘Wushancuili'underwent a remarkable orthoselection during evolution.Gene identification revealed that loss-of-function in four core MYB10 genes results in the anthocyanin deficiency and absence of red color,revealing the green coloration due to the residual high chlorophyll in fruit skin.Besides,the occurrence of cracking is assumed to be closely associated with cell wall modification and frequently rain-induced pathogen enrichment through transcriptomic analysis.The loss of MYB10 genes might render fruit more susceptible to pathogen-mediated cracking by weakening the epidermal strength and reactive oxygen species(ROS)scavenging.Our findings provided fundamental knowledge regarding fruit coloration and rain-cracking and will facilitate genetic improvement and cultivation management in Chinese plums.

关键词： Chinese plum Fruit coloration Fruit epidermis Genome MYB10 Rain-cracking

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A tunable Genome editing system of the prime editor mediated by dihydrofolate reductase

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Journal of Genetics and Genomics 2023年第3期50卷 204-207页

作者： Shu Liu Xiaoyue Duan Feng Peng Yafang Wang Yang Liu Xiaoling Wan Jingfa Zhang Xiaosa Li Xiaodong Sun Department of Ophthalmology Shanghai General Hospital(Shanghai First People’s Hospital)Shanghai Jiao Tong University School of MedicineShanghai 200080China Department of Ophthalmology Shanghai Changhai HospitalShanghai 200043China Shanghai Key Laboratory of Ocular Fundus Diseases 100 Haining RoadShanghai 200080China

The clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(CRISPR/Cas)system was discovered in bacteria and archaea as an adaptive immunity system to protect against exogenous DNA(Barrangou et al.,2007).This system has been developed into a powerful gene editing tool for eukaryotic Genome manipulation that has therapeutic opportunities against hereditary diseases(Cong et al.,2013),especially monogenic diseases.

关键词： CRISPR/Cas Genome system

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Initiation of the Primate Genome Project

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Zoological Research 2022年第2期43卷 147-149页

作者： Dong-Dong Wu Xiao-Guang Qi Li Yu Ming Li Zhi-Jin Liu Anne DYoder Christian Roos Takashi Hayakawa Jeffrey Rogers Tomas Marques-Bonet Bing Su Yong-Gang Yao Ya-Ping Zhang Guojie Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China National Resource Center for Non-Human Primates Kunming Primate Research Centerand National Research Facility for Phenotypic&Genetic Analysis of Model Animals(Primate Facility)Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650107China Kunming Natural History Museum of Zoology Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Shaanxi Key Laboratory for Animal Conservation College of Life SciencesNorthwest UniversityXi’anShaanxi 710069China State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Yunnan UniversityKunmingYunnan 650091China CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Department of Biology Duke UniversityDurhamNC 27708USA Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGöttingen 37077Germany Faculty of Environmental Earth Science Hokkaido UniversitySapporoHokkaido 060-0810Japan Japan Monkey Centre InuyamaAichi 484-0081Japan Human Genome Sequencing Center Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX 77030USA Institute of Evolutionary Biology(UPF-CSIC) PRBBDr.Aiguader 88Barcelona 08003Spain Catalan Institution of Research and Advanced Studies(ICREA) Passeig de Lluis Companys23Barcelona 08010Spain CNAG-CRG Centre for Genomic Regulation(CRG)Barcelona Institute of Science and Technology(BIST)Baldiri i Reixac 4Barcelona 08028Spain Institut Catalade Paleontologia Miquel Crusafont Universitat Autonoma de BarcelonaEdifici ICTA-ICPc/Columnes s/nCerdanyola del VallèsBarcelona 08193Spain Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese

A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in Genome sequencing due to its unique phylogenetic position and key importance.

关键词： Genome evolution condition.

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