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genome assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)

Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1106-1118页

作者： Yinqing Yang Kang Zhang Ya Xiao Lingkui Zhang Yile Huang Xing Li Shumin Chen Yansong Peng Shuhua Yang Yongbo Liu Feng Cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China Biotechnology Research Center Xiangxi Academy of Agricultural SciencesJishou 416000China Lushan Botanical Garden Chinese Academy of SciencesJiujiang 332900China State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment Chinese Research Academy of Environmental SciencesBeijing 100012China

Rubus corchorifolius(Shanmei or mountain berry,2n=14)is widely distributed in China,and its fruits possess high nutritional and medicinal ***,we reported a highquality chromosome-scale genome assembly of Shanmei,with contig size of 215.69 Mb and 26,696 *** comparison among Rosaceae species showed that Shanmei and Fupenzi(Rubus chingii Hu)were most closely related,followed by blackberry(Rubus occidentalis),and that environmental adaptation-related genes were expanded in the Shanmei *** resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan,Hunan,Jiangxi,and Sichuan in China revealed that among these samples,the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral ***,the Yunnan population underwent strong selection based on the nucleotide diversity,linkage disequilibrium,and historical effective population size ***,genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways,indicating the genetic basis of adaptation of Shanmei to the local *** high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

关键词： Rubus corchorifolius genome assembly Resequencing Divergence genome evolution

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genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

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The Crop Journal 2022年第1期10卷 47-55页

作者： Fei Ge Jingtao Qu Peng Liu Lang Pan Chaoying Zou Guangsheng Yuan Cong Yang Guangtang Pan Jianwei Huang Langlang Ma Yaou Shen Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina Berry Genomics Corporation Beijing 100015China

The current assembled maize genomes cannot represent the broad genetic diversity of maize *** more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in *** we describe the genome sequence and annotation of A188,a maize inbred line with high phenotypic variation relative to other lines,acquired by single-molecule sequencing and optical genome *** assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases(Mb),compared to 9.73 Mb for B73 and 10.2 Mb for *** on the B73_Ref Gen_V4 genome,295 scaffolds(2084.35 Mb,94.30%of the final genome assembly)were anchored and oriented on ten *** analysis revealed that~30%of the predicted A188 genes showed large structural divergence from B73,Mo17,and W22 genomes,which causes high protein divergence and may lead to phenotypic variation among the four inbred *** a line with high embryonic callus(EC)induction capacity,A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in *** our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.

关键词： Maize Embryonic callus A188 genome assembly Single-molecule sequencing

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genome assembly of KA105,a new resource for maize molecular breeding and genomic research

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The Crop Journal 2023年第6期11卷 1793-1804页

作者： Ting Li Shutu Xu Jiawen Zhao Yapeng Wang Jun Zhang Xin Wei Jianzhou Qu Ruisu Yu Xinghua Zhang Chuang Ma Jiquan Xue The Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region Northwest A&F UniversityYangling 712100ShaanxiChina Maize Engineering&Technology Research Centre College of AgronomyNorthwest A&F UniversityYangling 712100ShaanxiChina State Key Laboratory of Crop Stress Biology for Arid Areas Center of BioinformaticsCollege of Life SciencesNorthwest A&F UniversityYangling 712100ShaanxiChina

Superior inbred lines are central to maize breeding as sources of natural *** many elite lines have been sequenced,less sequencing attention has been paid to newly developed *** constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for *** pedigree showed genetic divergence from B73 and other lines in its *** with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight *** than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel *** KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

关键词： genome assembly Pedigree analysis Structural variation Transcriptome atlas Differential network

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genome assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 14-28页

作者： Ruicai Long Fan Zhang Zhiwu Zhang Mingna Li Lin Chen Xue Wang Wenwen Liu Tiejun Zhang Long-Xi Yu Fei He Xueqian Jiang Xijiang Yang Changfu Yang Zhen Wang Junmei Kang Qingchuan Yang Institute of Animal Sciences Chinese Academy of Agricultural SciencesBeijing 100193China Department of Crop and Soil Sciences Washington State UniversityPullmanWA 99163USA School of Grassland Science Beijing Forestry UniversityBeijing 100083China United States Department of Agriculture-Agricultural Research Service Plant and Germplasm Introduction and Testing ResearchProsserWA 99350USA

Alfalfa(Medicago sativa L.)is the most important legume forage crop worldwide with high nutritional value and *** a long time,the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic *** herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4,a cultivar widely cultivated in China,and a comprehensive database of genomic variations based on resequencing of 220 *** 2.74 Gb contigs(N50 of 2.06 Mb),accounting for 88.39%of the estimated genome,were assembled,and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes.A total of 34,922 allelic genes were identified from the allele-aware *** observed the expansion of gene families,especially those related to the nitrogen metabolism,and the increase of repetitive elements including transposable elements,which probably resulted in the increase of Zhongmu-4 genome compared with Medicago *** structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe,suggesting that geography may influence alfalfa genetic divergence during local ***-wide association studies identified 101 single nucleotide polymorphisms(SNPs)associated with 27 agronomic *** candidate genes were predicted to be correlated with fall dormancy and salt *** believe that the alleleaware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.

关键词： Alfalfa Autotetraploid genome assembly Resequencing genome-wide association study

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genome assembly and transcriptome analysis provide insights into the antischistosome mechanism of Microtus fortis

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Journal of Genetics and Genomics 2020年第12期47卷 743-755页

作者： Hong Li Zhen Wang Shumei Chai Xiong Bai Guohui Ding Yuanyuan Li Junyi Li Qingyu Xiao Benpeng Miao Weili Lin Jie Feng Mingyue Huang Cheng Gao Bin Li Wei Hu Jiaojiao Lin Zhiqiang Fu Jianyun Xie Yixue Li Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Animal ParasitologyMinistry of AgricultureShanghai 200241China Shanghai Laboratory Animal Research Center Shanghai 201203China Institute for Digital Health International Human Phenome Institutes(Shanghai)Shanghai 200433China Shanghai Center for Bioinformation Technology Shanghai Academy of Science and TechnologyShanghai 201203China School of Computer Science and Technology Harbin Institute of Technology(Shenzhen)ShenzhenGuangdong 518055China Shanghai Institute of Immunology Department of Immunology and MicrobiologyShanghai JiaoTong University School of MedicineShanghai 200025China State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Contemporary AnthropologyCollaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200438China Hangzhou Institute for Advanced Study University of Chinese Academy of SciencesHangzhouZhejiang 330106China

Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum ***,the underlying molecular mechanisms of this resistance are not yet ***,we perform the first de novo genome assembly of ***,comprehensive gene annotation analysis,and evolution ***,we compare the recovery rate of schistosomes,pathological changes,and liver transcriptomes between *** and mice at different time points after *** observe that the time and type of immune response in *** are different from those in *** activates immune and inflammatory responses on the 10th day post infection,such as leukocyte extravasation,antibody activation,Fc-gamma receptor-mediated phagocytosis,and the interferon signaling cascade,which play important roles in preventing the development of *** contrast,an intense immune response occurrs in mice at the late stages of infection and could not eliminate *** mice suffer severe pathological injury and continuous decreases in cell cycle,lipid metabolism,and other *** findings offer new insights into the intrinsic resistance mechanism of *** against schistosome *** genome sequence also provides the basis for future studies of other important traits in ***.

关键词： genome assembly Microtus fortis Schistosome Immune Transcriptome

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A Chromosome-level genome assembly of Wild Castor Provides New Insights into Its Adaptive Evolution in Tropical Desert

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 42-59页

作者： Jianjun Lu Cheng Pan Wei Fan Wanfei Liu Huayan Zhao Donghai Li Sen Wang Lianlian Hu Bing He Kun Qian Rui Qin Jue Ruan Qiang Lin Shiyou Lü Peng Cui CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhan 430074China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China University of Chinese Academy of Sciences Beijing 100049China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan 434200China

Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry *** investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,*** with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress *** variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision ***,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme *** identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.

关键词： Ricinus communis L. Adaptive evolution Selection signature Genetic variation genome assembly

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Gapless genome assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

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Rice science 2024年第3期31卷 317-327,I0042-I0045页

作者： LI Dian DUAN Wenjing LIU Qun’en WU Weixun ZHAN Xiaodeng SUN Lianping ZHANG Yingxin CHENG Shihua State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China

Accurate genomic information is essential for advancing genetic breeding research in specific rice *** study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene ***,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)*** transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH *** analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall *** results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid *** association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH *** summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

关键词： brown planthopper gapless genome genome assembly multi-omics Nilaparvata lugens rice

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RGAAT: A Reference-based genome assembly and Annotation Tool for New genomes and Upgrade of Known genomes

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 373-381页

作者： Wanfei Liu Shuangyang Wu Qiang Lin Shenghan Gao Feng Ding Xiaowei Zhang Hasan Awad Aljohi Jun Yu Songnian Hu CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Joint Center for Genomics Research(JCGR) King Abdulaziz City for Science and Technology and Chinese Academy of SciencesRiyadh 11442Saudi Arabia University of Chinese Academy of Sciences Beijing 100049China Grail Scientific Co.Ltd. Shenyang 110000China Shenzhen Institute of Geriatrics Shenzhen 518020China

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://***/projects/rgaat/and https://***/wushyer/RGAAT;2 at no cost.

关键词： Variant identification genome assembly genome annotation genome comparison

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A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus(JUJUNCAO)provides insights into its evolution and C4 photosynthesis

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Plant Communications 2023年第5期4卷 324-341页

作者： Huakun Zheng Baiyu Wang Xiuting Hua Ruiting Gao Yuhao Wang Zixin Zhang Yixing Zhang Jing Mei Yongji Huang Yumin Huang Hui Lin Xingtan Zhang Dongmei Lin Siren Lan Zhongjian Liu Guodong Lu Zonghua Wang Ray Ming Jisen Zhang Zhanxi Lin National Engineering Research Center of JUNCAO Technology College of Life ScienceFujian Agriculture and Forestry UniversityFuzhou 350002China State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources Guangxi Key Laboratory of Sugarcane BiologyGuangxi UniversityNanning 530004GuangxiChina Center for Genomics Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhou 350002China Fuzhou Institute of Oceanography Minjiang UniversityFuzhou 350108China

JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel ***,we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated2.7 million years ago(mya).Its genome consists of two subgenomes,and subgenome A shares high collinear synteny with pearl *** also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of *** transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes,which was a further indication of asymmetric DNA *** three types of centromeric repeat in the JUJUNCAO genome(CEN137,CEN148,and CEN156)may have evolved independently within each subgenome,with some introgressions of CEN156 from the B to the A *** investigated the photosynthetic characteristics of JUJUNCAO,revealing its typical C4 Kranz anatomy and high photosynthetic ***-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO,which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass *** together,our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies,as well as genetic improvement of Cenchrus grasses.

关键词： genome assembly allotetrapolyploid centromere architecture evolutionary trajectory photosynthetic efficiency Cenchrus grass

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GAEP:a comprehensive genome assembly evaluating pipeline

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Journal of Genetics and Genomics 2023年第10期50卷 747-754页

作者： Yong Zhang Hong-Wei Lu 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 SciencesShenzhenGuangdong 518120China State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhouZhejiang 311401China

With the rapid development of sequencing technologies,especially the maturity of third-generation sequencing technologies,there has been a significant increase in the number and quality of published genome *** emergence of these high-quality genomes has raised higher requirements for genome *** numerous computational methods have been developed to evaluate assembly quality from various perspectives,the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly *** address this issue,we have developed the genome assembly Evaluating Pipeline(GAEP),which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives,including continuity,completeness,and ***,GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy,which performs well in our *** is publicly available at https://***/zyoptimistic/GAEP under the GPL3.0 *** GAEP,users can quickly obtain accurate and reliable evaluation results,facilitating the comparison and selection of high-quality genome assemblies.

关键词： genome assembly assembly quality assembly metrics assembly evaluation pipeline Misassembly detection Misassembly breakpoint assembly redundancy

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