Taxonomic structure and functional association of foxtail millet root microbiome.
Tao Jin,Yayu Wang,Yueying Huang,Jin Xu,Pengfan Zhang,Nian Wang,Xin Liu,Haiyan Chu,Guang Liu,Honggang Jiang,Yuzhen Li,Jing Xu,Karsten Kristiansen,Liang Xiao,Yunzeng Zhang,Gengyun Zhang,Guohua Du,Houbao Zhang,Hongfeng Zou,Zhang Haifeng,Zhuye Jie,Suisha Liang,Huijue Jia,Jingwang Wan,Dechun Lin,Jinying Li,Guangyi Fan,Huanming Yang,Jian Wang,Yang Bai,Xun Xu +30 more
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TLDR
The results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane in foxtail millet root bacterial community, and may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.Abstract:
The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16 109 operational taxonomic units (OTUs), and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community. We systematically described the root bacterial community structure of foxtail millet and found its core rhizoplane bacterial members. Our results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane. The potentially beneficial bacteria may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.read more
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Multi-platform discovery of haplotype-resolved structural variation in human genomes
Mark Chaisson,Mark Chaisson,Ashley D. Sanders,Xuefang Zhao,Xuefang Zhao,Ankit Malhotra,David Porubsky,David Porubsky,Tobias Rausch,Eugene J. Gardner,Oscar L. Rodriguez,Li Guo,Ryan L. Collins,Xian Fan,Jia Wen,Robert E. Handsaker,Robert E. Handsaker,Susan Fairley,Zev N. Kronenberg,Xiangmeng Kong,Fereydoun Hormozdiari,Dillon Lee,Aaron M. Wenger,Alex Hastie,Danny Antaki,Thomas Anantharaman,Peter A. Audano,Harrison Brand,Stuart Cantsilieris,Han Cao,Eliza Cerveira,Chong Chen,Xintong Chen,Chen-Shan Chin,Zechen Chong,Nelson T. Chuang,Christine C. Lambert,Deanna M. Church,Laura Clarke,Andrew Farrell,Joey Flores,Timur R. Galeev,David U. Gorkin,David U. Gorkin,Madhusudan Gujral,Victor Guryev,William Haynes Heaton,Jonas Korlach,Sushant Kumar,Jee Young Kwon,Ernest T. Lam,Jong Eun Lee,Joyce V. Lee,Wan-Ping Lee,Sau Peng Lee,Shantao Li,Patrick Marks,Karine A. Viaud-Martinez,Sascha Meiers,Katherine M. Munson,Fabio C. P. Navarro,Bradley J. Nelson,Conor Nodzak,Amina Noor,Sofia Kyriazopoulou-Panagiotopoulou,Andy Wing Chun Pang,Yunjiang Qiu,Yunjiang Qiu,Gabriel Rosanio,Mallory Ryan,Adrian M. Stütz,Diana C.J. Spierings,Alistair Ward,Anne Marie E. Welch,Ming Xiao,Wei Xu,Chengsheng Zhang,Qihui Zhu,Xiangqun Zheng-Bradley,Ernesto Lowy,Sergei Yakneen,Steven A. McCarroll,Steven A. McCarroll,Goo Jun,Li Ding,Chong-Lek Koh,Bing Ren,Bing Ren,Paul Flicek,Ken Chen,Mark Gerstein,Pui-Yan Kwok,Peter M. Lansdorp,Peter M. Lansdorp,Peter M. Lansdorp,Gabor T. Marth,Jonathan Sebat,Xinghua Shi,Ali Bashir,Kai Ye,Scott E. Devine,Michael E. Talkowski,Michael E. Talkowski,Ryan E. Mills,Tobias Marschall,Jan O. Korbel,Evan E. Eichler,Charles Lee +107 more
TL;DR: A suite of long-read, short- read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms are applied to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner.
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GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
T. Rhyker Ranallo-Benavidez,Kamil S. Jaron,Kamil S. Jaron,Michael C. Schatz,Michael C. Schatz +4 more
TL;DR: A practical implementation of the polyploid-aware mixture model that quickly and accurately infers genome properties across thousands of simulated and several real datasets spanning a broad range of complexity is described and evaluated.
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Multiple wheat genomes reveal global variation in modern breeding.
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TL;DR: Comparative analysis of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.
Journal ArticleDOI
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals
Stefania Vaga,Sunjae Lee,Boyang Ji,Anna Andreasson,Anna Andreasson,Anna Andreasson,Nicholas J. Talley,Lars Agréus,Gholamreza Bidkhori,Petia Kovatcheva-Datchary,Petia Kovatcheva-Datchary,Jun-Seok Park,Doheon Lee,Gordon Proctor,Stanislav Dusko Ehrlich,Jens Nielsen,Lars Engstrand,Saeed Shoaie,Saeed Shoaie +18 more
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