|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding显示文摘Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs. | Xiaoya Shi Shuo Cao Xu Wang Siyang Huang Yue Wang Zhongjie Liu Wenwen Liu Xiangpeng Leng Yanling Peng Nan Wang Yiwen Wang Zhiyao Ma Xiaodong Xu Fan Zhang Hui Xue Haixia Zhong Yi Wang Kekun Zhang Amandine Velt Komlan Avia Daniela Holtgräwe Jérôme Grimplet JoséTomás Matus Doreen Ware Xinyu Wu Haibo Wang Chonghuai Liu Yuling Fang Camille Rustenholz Zongming Cheng Hua Xiao Yongfeng Zhou | 2023 | Horticulture Research2023，10，5： | 3 |
| 2 | quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification显示文摘A high-quality genome is the basis for studies on functional,evolutionary,and comparative genomics.The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences,along with the emergence of a new‘telomere-to-telomere(T2T)assembly’era.However,the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited.Here,we developed a user-friendly web toolkit,quarTeT,which currently includes four modules:AssemblyMapper,GapFiller,TeloExplorer,and CentroMiner.First,AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome.Then,GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences.Finally,TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome.These four modules can be used alone or in combination with each other for T2T genome assembly and characterization.As a case study,by adopting the entire modular functions of quarTeT,we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0,which was assembled with the addition of manual handling.Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods.Collectively,quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration. | Yunzhi Lin Chen Ye Xingzhu Li Qinyao Chen Ying Wu Feng Zhang Rui Pan Sijia Zhang Shuxia Chen Xu Wang Shuo Cao Yingzhen Wang Yi Yue Yongsheng Liu Junyang Yue | 2023 | Horticulture Research2023，10，8： | 0 |
| 3 | A telomere-to-telomere genome assembly of Zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max显示文摘Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history.Nevertheless,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into soybean.Here,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong reads.We employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly accuracy.The assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference genome.Our annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are novel.ZH13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier assemblies.Specifically,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic diversity.In summary,we deliver the first complete Chinese soybean cultivar T2T genome.The comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution. | Anqi Zhang Tangchao Kong Baiquan Sun Shizheng Qiu Jiahe Guo Shuyong Ruan Yu Guo Jirui Guo Zhishuai Zhang Yue Liu Zheng Hu Tao Jiang Yadong Liu Shuqi Cao Shi Sun Tingting Wu Huilong Hong Bingjun Jiang Maoxiang Yang Xiangyu Yao Yang Hu Bo Liu Tianfu Han Yadong Wang | 2024 | The Crop Journal2024，12，1： | 0 |
| 4 | 基于国内外期刊论文分析全球猕猴桃研究与应用进展显示文摘依据科瑞唯安公司Web of Science核心合集和中国知网平台(CNKI)期刊数据库,重点对2003-2022年期间的SCI和CNKI核心期刊收录的猕猴桃(Actinidia)研究论文5320篇,采用文献计量分析方法,从论文发表年限、发表国家或地区分布、学科领域等方面进行统计分析,并对各学科领域的研究进展进行归纳总结。结果显示,20年内SCI和CNKI核心期刊文献数量总体呈增长趋势,SCI论文收录量最多的国家是中国,其次是新西兰、意大利等;CNKI核心期刊收录论文数量最多的机构是西北农林科技大学,其次是中国科学院武汉植物园和江西农业大学。猕猴桃研究涉及植物科学、园艺学、植物病理学和昆虫学、果品贮藏与加工学、分子生物学、生物化学、药物学、生物信息学等131个学科,很多论文来自跨学科研究。近5年发展最快的学科是分子生物学、植物病理学以及果品贮藏与加工学。本文通过对期刊论文的分析,旨在为我国科研人员了解全球猕猴桃研究动态、确立未来研究方向、开展学术交流提供信息和借鉴。 | 钟彩虹 黄文俊 赵婷婷 张吉 李黎 李大卫 张琼 田华 | 2023 | 植物科学学报2023，41，6： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员