The revolution of genome sequencing is continuing after the successful secondgeneration sequencing （SGS） technology. The third-generation sequencing （TGS） technology, led by Pacific Biosciences （PacBio）, is prog...The revolution of genome sequencing is continuing after the successful secondgeneration sequencing （SGS） technology. The third-generation sequencing （TGS） technology, led by Pacific Biosciences （PacBio）, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies （ONT）. MiniON identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MiniON has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assem- bly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.展开更多
The Asteraceae (Compositae),a large plant family of approximately 24 000-35 000 species,accounts for^10% of all angiosperm species and contributes a lot to plant diversity.The most representative members of the Astera...The Asteraceae (Compositae),a large plant family of approximately 24 000-35 000 species,accounts for^10% of all angiosperm species and contributes a lot to plant diversity.The most representative members of the Asteraceae are the economically important chrysanthemums (Chrysanthemum L.)that diversified through reticulate evolution.Biodiversity is typically created by multiple evolutionary mechanisms such as wholegenome duplication 0NGD)or polyploidization and locally repetitive genome expansion.However,the lack of genomic data from chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification.Here,we used Oxford Nanopore long-read technologyto sequence the diploid Chrysanthemum nankingense genome,which represents one of the progenitor genomes of domesticated chrysanthemums.Our analysis revealed that the evolution of the C.nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recentWGD that distinguishes chrysanthemum from sunflower,which diverged from chrysanthemum approximately 38.8 million years ago.Variations of ornamental and medicinal traits in chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication.Collectively,our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of chrysanthemum plants,and also to accelerate their breeding and improvement.展开更多
The pore structures and controlling factors of several different Paleozoic shales from Southern China and their kerogens were studied using nitrogen adsorption and scanning electron microscopy methods. The results ind...The pore structures and controlling factors of several different Paleozoic shales from Southern China and their kerogens were studied using nitrogen adsorption and scanning electron microscopy methods. The results indicate that： 1） The specific surface area is 2.22-3.52 m2/g and has no correlation with the TOC content of the Permian Dalong Formation shales, nanopores are extremely undeveloped in the Dalong Formation kerogens, which have specific surface areas of 20.35-27.49 me/g; 2） the specific surface area of the Silurian Longmaxi Formation shales is in the range of 17.83-29.49 m2/g and is positively correlated with TOC content, the kerogens from the Longmaxi Formation have well-developed nanopores, with round or elliptical shapes, and the specific surface areas of these kerogens are as high as 279.84-300.3 m2/g; 3） for the Niutitang Formation shales, the specific surface area is 20.12-29.49 m2/grock and increases significantly with increasing TOC and smectite content. The Niuti- tang Formation kerogens develop a certain amount of nanopores with a specific surface area of 161.2 m2/g. Oil shale was also examined for comparison, and was found to have a specific surface area of 19.99 m2/g. Nanopores are rare in the Youganwo Formation kerogen, which has a specific surface area of only 5.54 m2/g, suggesting that the specific surface area of oil shale is due mainly to the presence of smectite and other clay minerals. The specific surface area and the number of pores present in shales are closely related to TOC, kerogen type and maturity, smectite content, and other factors. Low-maturity kerogen has very few nanopores and therefore has a very low specific surface area, whereas nanopores are abundant in mature to over- mature kerogen, leading to high specific surface areas. The Longmaxi Formation kerogen has more developed nanopores and a higher specific surface area than the Niutitang Formation kerogen, which may be due to differences in the kerogen type and maceral components. A high content of smectite may a展开更多
The pores in shales are mainly of nanometer-scale, and their pore size distribution is very important for the preservation and exploitation of shale gas. This study focused on the organic-rich Lower Silurian black sha...The pores in shales are mainly of nanometer-scale, and their pore size distribution is very important for the preservation and exploitation of shale gas. This study focused on the organic-rich Lower Silurian black shale from four wells in the Upper Yangtze Platform, and their TOC, mineralogical composition and pore characterization were investigated. Low pressure N2 and CO2 adsorption were conducted at 77.35 K and 273.15 K, respectively, and the pore structures were characterized by modified Brunauer-Emmett-Teller （BET）, Dubinin-Radushkevich （DR）, t-plot, Barrett- Joyner-Halenda （BJH） and density functional theory （DFT） methods and then the relationship between pore structure and shale gas sorption capacity was discussed. The results indicate that （1） The Lower Silurian shale has high TOC content of 0.92%~96%, high quartz content of 30.6%-69.5%, and high clays content of 24.1%-51.2%. The total specific surface area varies from 7.56 m^2/g to 25.86 m^2/g. Both the total specific surface area and quartz content are positively associated with the TOC content. （2） Shale samples with higher TOC content have more micropores, which results in more complex nanopore structure. Micropore volumes/surface areas and non-micropore surface areas all increase with the increasing TOC content. （3） A combination of N2 and CO2 adsorption provides the most suitable detection range （~0.3-60 nm） and has high reliability and accuracy for nanopore structure characterization. （4） The TOC content is the key factor to control the gas sorption capacity of the Lower Silurian shale in the Upper Yangtze Platform.展开更多
Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The...Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein.Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale.In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.展开更多
Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly ...Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.展开更多
基金supported by the Wellcome Trust,the United Kingdom
文摘The revolution of genome sequencing is continuing after the successful secondgeneration sequencing （SGS） technology. The third-generation sequencing （TGS） technology, led by Pacific Biosciences （PacBio）, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies （ONT）. MiniON identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MiniON has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assem- bly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.
基金The National Key Research and Development Program of China (2016YFD0801102)and the National Natural Science Foundation of China (31870198 and 31400278).
文摘The Asteraceae (Compositae),a large plant family of approximately 24 000-35 000 species,accounts for^10% of all angiosperm species and contributes a lot to plant diversity.The most representative members of the Asteraceae are the economically important chrysanthemums (Chrysanthemum L.)that diversified through reticulate evolution.Biodiversity is typically created by multiple evolutionary mechanisms such as wholegenome duplication 0NGD)or polyploidization and locally repetitive genome expansion.However,the lack of genomic data from chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification.Here,we used Oxford Nanopore long-read technologyto sequence the diploid Chrysanthemum nankingense genome,which represents one of the progenitor genomes of domesticated chrysanthemums.Our analysis revealed that the evolution of the C.nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recentWGD that distinguishes chrysanthemum from sunflower,which diverged from chrysanthemum approximately 38.8 million years ago.Variations of ornamental and medicinal traits in chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication.Collectively,our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of chrysanthemum plants,and also to accelerate their breeding and improvement.
基金supported by National Basic Research Program of China(Grant No.2012CB214704)Major National Science and Techno-logy Project(Grant No.2011ZX05008-002-20)National Natural Science Foundation of China(Grant No.4123058)
文摘The pore structures and controlling factors of several different Paleozoic shales from Southern China and their kerogens were studied using nitrogen adsorption and scanning electron microscopy methods. The results indicate that： 1） The specific surface area is 2.22-3.52 m2/g and has no correlation with the TOC content of the Permian Dalong Formation shales, nanopores are extremely undeveloped in the Dalong Formation kerogens, which have specific surface areas of 20.35-27.49 me/g; 2） the specific surface area of the Silurian Longmaxi Formation shales is in the range of 17.83-29.49 m2/g and is positively correlated with TOC content, the kerogens from the Longmaxi Formation have well-developed nanopores, with round or elliptical shapes, and the specific surface areas of these kerogens are as high as 279.84-300.3 m2/g; 3） for the Niutitang Formation shales, the specific surface area is 20.12-29.49 m2/grock and increases significantly with increasing TOC and smectite content. The Niuti- tang Formation kerogens develop a certain amount of nanopores with a specific surface area of 161.2 m2/g. Oil shale was also examined for comparison, and was found to have a specific surface area of 19.99 m2/g. Nanopores are rare in the Youganwo Formation kerogen, which has a specific surface area of only 5.54 m2/g, suggesting that the specific surface area of oil shale is due mainly to the presence of smectite and other clay minerals. The specific surface area and the number of pores present in shales are closely related to TOC, kerogen type and maturity, smectite content, and other factors. Low-maturity kerogen has very few nanopores and therefore has a very low specific surface area, whereas nanopores are abundant in mature to over- mature kerogen, leading to high specific surface areas. The Longmaxi Formation kerogen has more developed nanopores and a higher specific surface area than the Niutitang Formation kerogen, which may be due to differences in the kerogen type and maceral components. A high content of smectite may a
基金the financial support of the National Science and Technology Major Project(No.2016ZX05034-001)National Natural Science Foundation of China(No.41472112)
文摘The pores in shales are mainly of nanometer-scale, and their pore size distribution is very important for the preservation and exploitation of shale gas. This study focused on the organic-rich Lower Silurian black shale from four wells in the Upper Yangtze Platform, and their TOC, mineralogical composition and pore characterization were investigated. Low pressure N2 and CO2 adsorption were conducted at 77.35 K and 273.15 K, respectively, and the pore structures were characterized by modified Brunauer-Emmett-Teller （BET）, Dubinin-Radushkevich （DR）, t-plot, Barrett- Joyner-Halenda （BJH） and density functional theory （DFT） methods and then the relationship between pore structure and shale gas sorption capacity was discussed. The results indicate that （1） The Lower Silurian shale has high TOC content of 0.92%~96%, high quartz content of 30.6%-69.5%, and high clays content of 24.1%-51.2%. The total specific surface area varies from 7.56 m^2/g to 25.86 m^2/g. Both the total specific surface area and quartz content are positively associated with the TOC content. （2） Shale samples with higher TOC content have more micropores, which results in more complex nanopore structure. Micropore volumes/surface areas and non-micropore surface areas all increase with the increasing TOC content. （3） A combination of N2 and CO2 adsorption provides the most suitable detection range （~0.3-60 nm） and has high reliability and accuracy for nanopore structure characterization. （4） The TOC content is the key factor to control the gas sorption capacity of the Lower Silurian shale in the Upper Yangtze Platform.
基金supported by the National Natural Science Foundation of China–China(Grant No.61471336)the Joint-Scholar of West Light Foundation of the Chinese Academy of Sciences awarded to DW and Shanghai Synchrotron Radiation FacilityCY was supported by China Postdoctoral Science Foundation–China(Grant No.2014M551011)
文摘Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein.Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale.In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.
基金supported by the National key research and development plan(2016TFC1202700,2016YFC1200900)Beijing Municipal Science&Technology Commission project(grant numbers D151100002115003)Guangzhou Municipal Science&Technology Commission project(grant numbers 2015B2150820)
文摘Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. Methods In this proof-of-concept study using Enterovirus 71 （EV71） and Coxsackievirus A16 （CA16） strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Results Within the first minute （min） of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min （on average）, 99% identity was achieved for 10 CA16 strains in a single run. Conclusion MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use.
