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Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

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Fundamental Research 2022年第6期2卷 946-953页

作者： Xiaofei Yang Xixi Zhao Shoufang Qu Peng Jia Bo Wang Shenghan Gao Tun Xu Wenxin Zhang Jie Huang Kai Ye genome Institute the First Affiliated Hospital of Xi'an Jiaotong UniversityXi'an 710061ShaanxiChina School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'an 710049ShaanxiChina MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'an 710049ShaanxiChina National Institutes for food and drug Control(NIFDC) No.2Tiantan XiliDongcheng DistrictBeijing 102629China School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi'an Jiaotong UniversityXi'an 710049ShaanxiChina School of Life Science and Technology Xi'an Jiaotong UniversityXi'an 710049ShaanxiChina Faculty of Science Leiden UniversityLeidenThe Netherlands

The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome *** this study,we sequenced a cell line named HJ,established from a Chinese Han male individual by using HiFi and *** assembled two high-quality haplotypes of the HJ genome(haplotype 1(H1):3.1 Gb,haplotype 2(H2):2.9 Gb).The continuity(H1:contig N50=28.2 Mb,H2:contig N50=25.9 Mb)and completeness(BUSCO:H1=94.9%,H2=93.5%)are substantially better than those of other Chinese genomes,for example,HX1,NH1.0,and *** comparing HJ genome with GRCh38,we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2,*** addition,we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2,*** results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.

关键词： genome assembly HiFi reads Human genome Haplotype-resolved Chinese Han Mutation landscape

Chromosome-scale genome assembly of the autoalloenneaploid Arundo donax

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Grassland Research 2024年第3期3卷 230-242页

作者： Mengmeng Ren Fupeng Liu Xiaohong Han Daohong Wu Hai Peng Wuhan Rundo Biotechnology Co.Ltd. WuhanHubeiChina 2Institute for Systems BiologyJianghan UniversityWuhanHubeiChina

Background:Arundo donax *** great potential as an energy crop due to its high biomass yield and broad adaptability,while lack of a reference genome is a hindrance to genetic improvement efforts for this ***:genome assembly of *** was conducted by utilizing PacBio SMRT sequencing and high-throughput chromosome conformation capture technology,with further analysis exploring the plant's ploidy,whole-genome duplication event,and evolutionary history through comparative ***:The genome assembly of *** consists of 1.30 Gb with a contig N50 size of 33.15 Mb.A total of 74403 gene models were identified,with over 90%of genes being functionally *** and synteny analyses revealed that *** is an autoalloenneaploid(3n=9x=108)and has experienced significant gene family expansion and two whole-genome duplication events during its evolutionary ***,utilizing the genome assembly,a variety of salinity stress-related genes were uncovered through the analysis of public RNA-seq ***:This study presents the initial chromosome-scale genome assembly of ***,which will advance genetic comprehension and support the genetic enhancement of this important energy crop.

关键词： Arundo donax autoallopolyploid comparative genomics genome assembly

Improved genome assembly of Chinese sucker(Myxocyprinus asiaticus)provides insights into the identification and characterization of pharyngeal teeth related maker genes in Cyprinoidei

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Water Biology and Security 2022年第3期1卷 18-27页

作者： Xin Liu Honghui Zeng Cheng Wang Jing Bo Xiaoni Gan Chengchi Fang Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan430072China University of Chinese Academy of Sciences Beijing100049China Institute of Deep Sea Science and Engineering Chinese Academy of SciencesSanya572000China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming650223China

The Chinese sucker,Myxocyprinus asiaticus(***,Catostomidae,Cypriniformes),is the only living species of Catostomidae in *** are more than 75 species of this family in North *** fossil record of this group dates back to the early *** the Chinese sucker is located at the base of the Cyprinoidei phylogeny,this species is also important in clarifying the evolutionary relationships within ***,we assembled a high-quality genome of the Chinese sucker,contig N50(40.26 Mb),which is nearly ten times longer than the previous version(4.19 Mb).Phylogenetic analysis identified that Chinese sucker together with Cyprinidae groups are paraphyletic with respect to *** specific whole genome duplication event of the Chinese sucker was estimated to have occurred~25.9 million years *** of population historical changes indicated a trend of reduction for the Chinese sucker and *** Dlx genes play a key role in Cypriniformes pharyngeal teeth development,we conducted a genome-wide identification of Dlx genes,and found that these genes were doubled in whole genome duplication events,followed by the loss of specific *** results showed that the expression levels of these paralogous genes were *** genomic resource provides useful information for the protection of Chinese sucker and functional study of Dlx genes.

关键词： Chinese sucker Catostomidae genome assembly genome duplication Dlx gene

An Asynchronous Parallel Model for genome assembly

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An Asynchronous Parallel Model for Genome Assembly

Construction and application of a high-density cytogenetic map in sesame(Sesamum indicum L.) for genome assembly

第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Jintao Meng Shengzhong Feng Yanjie Wei Institute of Computing Technology Chinese Academy of Sciences Center for High Performance Computing Shenzhen Institutes of Advanced TechnologyChinese Academy of Sciences

Background:Current sequencing technology(Illumina Solexa,Applied Biosystems SoLiD,and Helicos Biosciences Heliscope etc.) allows one to read millions of 35 to 100 nucleotide sequences per *** to experimental errors,gaps,and genomic repeats,a much higher coverage depth of 50-fold to 300-fold is needed for accurate *** factors contribute to a 300-fold to 1000-fold increase in the number of reads,resulting in billions of reads to be processed,which significantly complicates the genome assembly problem. Methods:This paper first demonstrates a multi-step bi-directed graph for the problem of genome *** can be recovered by merging semi-extended edges to fullextended edges or *** a small world asynchronous parallel(SWAP) model is proposed to realize edge merging over a distributed one-step bi-directed *** model applies the Lock-Computation-Unlock scheme to each vertex’s small ***,we implement an assembler named as Para-Assembler using the SWAP *** the number of processes p,the complexity of this problem is reduced to 0(n/p) parallel compute time, 0(n/p) communication round,and O(glog(g)/p) communication volume,here g is the length of genomes,and n is the number of nucleotide in all input reads. Results:Simulation results shows that Para-Assembler has a factor of 20 times speedup when the number of processors scales from 10 to 640. Conclusions:The proposed SWAP introduced local synchronization and global asynchronization mechanism to maximize the parallelism in the graph *** on SWAP model,we developed a new framework named as Para-assembler,and simulation results confirm its scalability over 640 *** Para-assembler can be used as basic computing framework for genome assembly.

关键词： parallel computing De Bruijn graph genome assembly

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Construction and application of a high-density cytogenetic m...

Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

中国作物学会油料作物专业委员会第八次会员代表大会暨学术年会

作者： ZHAO Rui-hong MIAO Hong-mei MA Qin LI Chun WEI Li-bin DUAN Ying-hui ZHANG Hai-yang Henan Sesame Research Center Henan Academy of Agricultural Sciences

Sesame is an important oilseed *** order to assemble the fine genome,a BAC library comprising 57 600 BAC clones for sesame was constructed,and the successive double-color fluorescence in situ hybridization(FISH) with bacterial artificial chromosomes(BACs) was *** on the nomination of 13 chromosome pairs in sesame somatic cells,a high-density cytogenetic map carrying 210 specific BACs was constructedfor the first *** 210 BACs were assigned onto 13 chromosome *** order to determine the relative position of BACs in chromosome,position of each BAC marker was calculated with more than triple *** value of each BAC ranged between 0.00 and *** of BAC marker each chromosome varied from 10 to *** results showed that the total size of 210 BAC located onto 51 scaffolds which covered more than 40%of sesame ***,BAC-FISH cytogenetic map was integrated with the super density SNP genetic map and applied to guide fine sesame genome *** cytogenetic map provides a solid foundation for sesame genome assembly and further genomic analysis.

关键词： sesame chromosome BAC-FISH cytogenetic map genome assembly

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Journal of Integrative Plant Biology 2022年第3期64卷 649-670页

作者： Yushan Zheng Deming Yang Jundong Rong Liguang Chen Qiang Zhu Tianyou He Lingyan Chen Jing Ye Lili Fan Yubang Gao Hangxiao Zhang Lianfeng Gu College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied PlantSystems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China

Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot *** genetic transformation and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing techniques are available for ***,enabling reverse genetic ***,*** has the potential to be a model bamboo ***,the genome sequence of *** has remained unreported due to its polyploidy and large genome ***,we sequenced the *** genome and assembled it into three allele-aware subgenomes(AABBCC),representingthe largest genome of a major bamboo *** assembled 70 allelic chromosomes(2,737 Mb)for hexaploid *** using both singlemolecule sequencing from the Pacific Biosciences(Pac Bio)Sequel platform and chromosome conformation capture sequencing(Hi-C).Repetitive sequences comprised 52.65%of the *** *** annotated 135231 protein-coding genes in the genome based on transcriptomes from eight different *** sequencing using RNA-Seq and Pac Bio singlemolecule real-time long-read isoform sequencing revealed highly differential alternative splicing(AS)between non-abortive and abortive shoots,suggesting that AS regulates the abortion rate of bamboo *** high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using *** as a model species.

关键词： alternative splicing bamboo shoots chromosome conformation capture sequencing D.latiflorus genome assembly single-molecular sequencing

Synthesis and assembly of full-length cyanophage A-4L genome

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Synthetic and Systems Biotechnology 2023年第1期8卷 121-128页

作者： Ting Zhang Bonan Xu Jia Feng Pingbo Ge Guorui Li Jiabao Zhang Jianting Zhou Jianlan Jiang School of Chemical Engineering and Technology Tianjin UniversityTianjin300072China Key Laboratory of Systems Bioengineering(Ministry of Education) Tianjin UniversityTianjin300072China Frontier Science Center for Synthetic Biology(Ministry of Education) Tianjin UniversityTianjin300072China

Artificial cyanophages are considered to be an effective biological method to control harmful cyanobacterial ***,no synthetic cyanophage genome has been constructed and where its obstacles are ***,we survey a stretch of 16 kb length sequence of cyanophage A-4L that is unclonable in Escherichia *** test 12 predicted promoters of cyanophage A-4L which were verified all active in ***,we screen for eight ORFs that hindered the assembly of intermediate DNA fragments in *** and describe that seven ORFs in the 16 kb sequence could not be separately cloned in *** of unclonable ORFs in high-copy-number plasmid were successfully cloned using low-copy-number vector,suggesting that these ORFs were *** propose a clone strategy abandoned the promotor and the start codon that could be applied for unclonable ***,we de novo synthesized and assembled the full-length genome of cyanophage *** work deepens the understanding of synthetic cyanophages studies.

关键词： genome assembly Cyanophage A-4L Toxic ORFs screening

A near-complete assembly of the Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in Yuxingcao

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Plant Communications 2024年第10期5卷 180-199页

作者： Zhengting Yang Fayin He Yingxiao Mai Sixian Fan Yin An Kun Li Fengqi Wu Ming Tang Hui Yu Jian-Xiang Liu Rui Xia Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China School of Life SciencesGuizhou Normal UniversityGuiyangGuizhou 550025China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of HorticultureSouth China Agricultural UniversityGuangzhouGuangdong 510640China Lishui Innovation Center for Life and Health Zhejiang UniversityHangzhou 310027China

Houttuynia cordata,also known as Yuxingcao in Chinese,is a perennial herb in the Saururaceae *** is highly regarded for its medicinal properties,particularly in treating respiratory infections and inflammatory conditions,as well as boosting the human immune ***,a lack of genomic information has hindered research on the functional genomics and potential improvements of *** this study,we present a near-complete assembly of *** genome and investigate the biosynthetic pathway of flavonoids,specifically quercetin,using genomics,transcriptomics,and metabolomics *** genome of *** diverged from that of Saururus chinensis around 33.4 million years ago;it consists of 2.24 Gb with 76 chromosomes(4n=76)and has undergone three whole-genome duplication(WGD)*** WGDs played a crucial role in shaping the *** genome and influencing the gene families associated with its medicinal *** metabolomics and transcriptomics analyses,we identified key genes involved in the b-oxidation process for biosynthesis of houttuynin,one of the volatile oils responsible for the plant’s fishy *** addition,using the reference genome,we identified genes involved in flavonoid biosynthesis,particularly quercetin metabolism,in *** discovery has important implications for understanding the regulatory mechanisms that underlie production of active pharmaceutical ingredients in traditional Chinese ***,the high-quality genome assembly of *** serves as a valuable resource for future functional genomics research and provides a solid foundation for genetic improvement of *** for the benefit of human health.

关键词： Houttuynia cordata flavonoid biosynthesis genome assembly houttuynin quercetin whole-genome duplication

Establishment of genome-editing system and assembly of a near-complete genome in broomcorn millet

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Journal of Integrative Plant Biology 2024年第8期66卷 1688-1702页

作者： Yang Liu Zixiang Cheng Weiyao Chen Chuanyin Wu Jinfeng Chen Yi Sui State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoologythe Chinese Academy of SciencesBeijing 100101China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China University of Chinese Academy of Sciences Beijing 100049China

The ancient crop broomcorn millet(Panicum miliaceum L.)is an indispensable orphan crop in semi-arid regions due to its short life cycle and excellent abiotic stress *** advantages make it an important alternative crop to increase food security and achieve the goal of zero hunger,particularly in light of the uncertainty of global climate ***,functional genomic and biotechnological research in broomcorn millet has been hampered due to a lack of genetic tools such as transformation and genome-editing ***,we successfully performed genome editing of broomcorn *** identified an elite variety,Hongmi,that produces embryogenic callus and has high shoot regeneration ability in in vitro *** established an Agrobacterium tumefaciens-mediated genetic transformation protocol and a clustered regularly interspaced short palindromic repeats(CRISPR)/Cas9-mediated genome-editing system for *** these techniques,we produced herbicide-resistant transgenic plants and edited phytoene desaturase(Pm PDS),which is involved in chlorophyll *** facilitate the rapid adoption of Hongmi as a model line for broomcorn millet research,we assembled a near-complete genome sequence of Hongmi and comprehensively annotated its ***,our results open the door to improving broomcorn millet using biotechnology.

关键词： broomcorn millet CRISPR/Cas9 editing genome assembly herbicide resistance transformation system