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De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation

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National Science Review 2020年第2期7卷 391-402页

作者： Ouzhuluobu Yaoxi He Haiyi Lou Chaoying Cui Lian Deng Yang Gao Wangshan Zheng Yongbo Guo Xiaoji Wang Zhilin Ning Jun Li Bin Li Caijuan Bai Baimakangzhuo Gonggalanzi Dejiquzong Bianba Duojizhuoma Shiming Liu Tianyi Wu Shuhua Xu Xuebin Qi Bing Su High Altitude Medical Research Center School of Medicine Tibetan University Fukang Obstetrics Gynecology and Children Branch Hospital Tibetan Fukang Hospital State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences Chinese Academy of Sciences Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational Biology Shanghai Institute of Nutrition and Health Shanghai Institutes for Biological SciencesUniversity of Chinese Academy of Sciences School of Life Science and Technology Shanghai Tech University Center for Disease Control Tibet Autonomous Region National Key Laboratory of High Altitude Medicine High Altitude Medical Research Institute Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Collaborative Innovation Center of Genetics and Development

structural variants(SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome(ZF1), with a contig N50 length of 24.57 mega-base pairs(Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps(0.25 Mb in total length) in the reference human genome(GRCh38). Markedly, we detected17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid(Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1(1.32%–1.53%) compared to other East Asian genomes(0.70%–0.98%),reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence—a662-bp intronic insertion in the SCUBE2 gene—is enriched and associated with better lung function(the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.

关键词： long-read sequencing Tibetan structural variants genetic adaptation reference genome

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Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species

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Zoological Research 2023年第2期44卷 287-302页

作者： Guang-Xian Tu Xin-Shuang Zhang Rui-Run Jiang Long Zhang Cheng-Jun Lai Zhu-Yue Yan Yan-Rong Lv Shao-Ping Weng Li Zhang Jian-Guo He Muhua Wang State Key Laboratory for Biocontrol School of Marine SciencesSun Yat-sen UniversityZhuhaiGuangdong 519000China China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)ZhuhaiGuangdong 519000China Chinese Institute for Brain Research Beijing 102206China Guangdong Province Key Laboratory for Aquatic Economic Animals School of Life SciencesSun Yat-sen UniversityGuangzhouGuangdong 510275China

Due to the difficulty in accurately identifying structural variants(SVs) across genomes,their impact on cisregulato ry diverge n ce of closely related species,especially fish,remains to be *** identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological ***,the role of broad H3K4me3 domains in phenotypic divergence remains poorly *** chuatsi and *** are closely related but divergent in several phenotypic traits,making them an ideal model to study cis-regulatory evolution in sister ***,we generated chromosome-level genomes of *** and ***,with assembled genome sizes of 716.35 and740.54 Mb,*** evolutionary histories of *** and *** were studied by inferring dynamic changes in ancestral population *** explore the genetic basis of adaptation in *** and ***,we performed gene family expansion and contraction analysis and identified positively selected genes(PSGs).To investigate the role of SVs in cis-regulatory divergence of closely related fish species,we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of *** and *** analysis revealed that cis-regulatory divergence caused by SVs played an essential role in phenotypic divergence between *** and ***,divergent broad H3K4me3 domains were mostly associated with cancer-related genes in *** and *** and contributed to their phenotypic divergence.

关键词： cis-regulatory divergence structural variants H3K27ac Broad H3K4me3 Siniperca chuatsi Siniperca scherzeri

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A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

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Plant Communications 2024年第2期5卷 261-278页

作者： Ning Guo Shenyun Wang Tianyi Wang Mengmeng Duan Mei Zong Liming Miao Shuo Han Guixiang Wang Xin Liu Deshuang Zhang Chengzhi Jiao Hongwei Xu Liyang Chen Zhangjun Fei Jianbin Li Fan Liu State Key Laboratory of Vegetable Biobreeding National Engineering Research Center for VegetablesBeijing Key Laboratory of Vegetable Germplasm ImprovementKey Laboratory of Biology and Genetics Improvement of Horticultural Crops(North China)Beijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry ScienceBeijing 100097China Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Vegetable Research InstituteJiangsu Academy of Agricultural ScienceNanjingJiangsuChina Smartgenomics Technology Institute Tianjin 301700China Boyce Thompson Institute IthacaNYUSA

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ *** we report a graph-based pan-genome of *** constructed from high-quality genome assemblies of different *** pan-genome harbors over 200 structural variant hotspot regions enriched in auxin-andflowering-related *** genomic analyses revealed that early domestication of *** focused on leaf or stem *** resulting from agricultural practices and variety improvement were detected among different ***-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAV-ATA3/ESR-RELATED family gene as crucial players in leaf–stem differentiation during the early stage of *** domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels *** pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization andflowering characteristics among different morphotypes,and variations in thefirst intron of BoFLC3 are involved infine-tuning theflowering process in *** study provides a comprehensive understanding of the pan-genome of *** and sheds light on the domestication and differential organ development of this globally important crop species.

关键词： Brassica oleracea graph-based pan-genome structural variants SV domestication morphotype diversification

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Whole-genome sequencing identifies novel genes for autism in Chinese trios

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Science China(Life Sciences) 2024年第11期67卷 2368-2381页

作者： Suhua Chang Jia Jia Liu Yilu Zhao Tao Pang Xiangyu Zheng Zhirui Song Anyi Zhang Xuping Gao Lingxue Luo Yanqing Guo Jing Liu Li Yang Lin Lu Peking University Sixth Hospital Peking University Institute of Mental HealthNHC Key Laboratory of Mental Health(Peking University)National Clinical Research Center for Mental Disorders(Peking University Sixth Hospital)Beijing 100191China Chinese Academy of Medical Sciences Research Unit(No.2018RU006) Peking UniversityBeijing 100191China School of Nursing Peking UniversityBeijing 100191China Wuhan Biobank Wuhan 430075China National Institute on Drug Dependence Peking UniversityBeijing 100191China

Autism spectrum disorder(ASD)is a neurodevelopmental disorder with high genetic heritability but *** understanding its genetics requires whole-genome sequencing(WGS),but the ASD studies utilizing WGS data in Chinese population are *** this study,we present a WGS study for 334 individuals,including 112 ASD patients and their non-ASD *** identified 146 de novo variants in coding regions in 85 cases and 60 inherited variants in coding *** integrating these variants with an association model,we identified 33 potential risk genes(Pvariants on the gene expression and found 12 genes in the individuals with the related variants had relatively biased *** further presented the clinical phenotypes of the proband carrying the risk genes in both our samples and Caucasian samples to show the effect of the risk genes on *** variants in noncoding regions,a total of 74 de novo variants and 30 inherited variants were predicted as pathogenic with high confidence,which were mapped to specific genes or regulatory *** number of de novo variants found in patient was significantly associated with the parents’ages at the birth of the child,and gender with *** also identified small de novo structural variants in ASD *** results in this study provided important evidence for understanding the genetic mechanism of ASD.

关键词： autism whole-genome sequencing de novo variants inherited variants SNV structural variants

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Irys:De Novo Assembly and structural Variation Detection in Complex Genomes Using Extremely Long Single-Molecule Imaging

Irys:De Novo Assembly and Structural Variation Detection in ...

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中国遗传学会第九次全国会员代表大会暨学术研讨会

作者： H VanSteenhouse A Hastie M Requa M Austin F Trintchouk M Saghbini X Yang H Cao BioNano Genomics Inc.

De novo genome assemblies using only short read data are generally incomplete and highly fragmented due to the intractable complexity found in most *** complexity, consisting mainly of large duplications and repetitive regions,hinders sequence assembly and subsequent comparative analyses. The lrys platform from BioNano Genomics overcomes the limitations of short fragment technologies to provide unprecedented insights into whole-genome *** is a single-molecule genome analysis system based on NanoChannel Array technology that linearizes extremely long DNA molecules for *** high-throughput platform automates massively parallel imaging of individual molecules of genomic DNA hundreds of kiiobases in size to measure sufficient sequence uniqueness and long-range contiguity critical for unambiguous de novo assembly of complex ***-resolution genome maps assembled de novo retain the original context and architecture of the genome,making them extremely useful for sequence assembly scaffolding and structural variation detection applications. Specifically,these genome maps provide dense genome-wide anchor points for ordering and orienting sequencing contigs or scaffolds to greatly increase completion and accuracy of de novo *** variants and repeats are measured directly within long "reads" for comprehensive analysis of what has been dubbed "the inaccessible genome".Following an introduction to the platform and underlying single-molecule technology,several examples of real-world application will demonstrate its use in large complex genomes.

关键词： Irys de novo assemblies structural variants

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Irys:de novo assembly and structural variation detection in complex genomes using extremely long single-molecule imaging

Irys:de novo assembly and structural variation detection in ...

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第十四届全国植物基因组学大会

作者： H VanSteenhouse A Hastie M Requa M Austin F Trintchouk M Saghbini X Yang H Cao BioNano Genomics Inc.

关键词： irys de novo assemblies structural variants

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lrys:De Novo Assembly and structural Variation Detection in Complex Genomes Using Extremely Long Single-Molecule Imaging

lrys:De Novo Assembly and Structural Variation Detection in ...

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中国遗传学会第九次全国会员代表大会暨学术研讨会

作者： H VanSteenhouse A Hastie M Requa M Austin F Trintchouk M Saghbini X Yang H Cao BioNano Genomics Inc.

De novo genome assemblies using only short read data are generally incomplete and highly fragmented due to the intractable complexity found in most *** complexity, consisting mainly of large duplications and repetitive regions,hinders sequence assembly and subsequent comparative analyses. The lrys platform from BioNano Genomics overcomes the limitations of short fragment technologies to provide unprecedented insights into whole-genome biology,lrys is a single-molecule genome analysis system based on NanoChannel Array technology that linearizes extremely long DNA molecules for *** high-throughput platform automates massively parallel imaging of individual molecules of genomic DNA hundreds of kilobases in size to measure sufficient sequence uniqueness and long-range contiguity critical for unambiguous de novo assembly of complex ***-resolution genome maps assembled de novo retain the original context and architecture of the genome,making them extremely useful for sequence assembly scaffolding and structural variation detection applications. Specifically,these genome maps provide dense genome-wide anchor points for ordering and orienting sequencing contigs or scaffolds to greatly increase completion and accuracy of de novo *** variants and repeats are measured directly within long "reads" for comprehensive analysis of what has been dubbed "the inaccessible genome".Following an introduction to the platform and underlying single-molecule technology,several examples of real-world application will demonstrate its use in large complex genomes.

关键词： Irys de novo assemblies structural variants

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