Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and h...Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.展开更多
Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.Thi...Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM(AM-314/MS-155)and alkali-tolerant genotype ALA(Alamo)as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method(Na2CO3:NaHCO3=1:9,C(Na+)=150 mmol·L-1 and pH=9.0)and fresh root samples were taken after treatments for 0(CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1%differentially expressed miRNAs was significantly down-regulated(p<0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.展开更多
【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact ...【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact of this soaking method on the fungal and bacterial community structures using next-generation sequencing technology(NGS).【Methods】Lily bulbs were soaked in a seed treating agent containing beneficial microbes(SP treatment)for 4 hours.Subsequently,they were planted in soil in July and sampled in September to assess plant growth,rhizosphere soil physicochemical properties,and microorganism community structures.In addition,we employed the software PICRUSt and FUNGuild to predict bacterial pathways and fungal functions.【Results】Under SP treatment,there were significant alterations in fungi and bacteria community structures,accompanied by improved soil nutrient status.Notably,the relative abundance of dominant microorganism groups,such as the fungi Basidiomycota,Pseudeurotium,Cladophialophora,Microascus,and Dactylonectria,as well as the bacteria Proteobacteria,Chloroflexi,Ochrobactrium,Lysobacter,and RB41,underwent notable changes.Microorganism function prediction results indicated a reduction in pathotrophic fungi(including plant pathogens)and an increase in endophytic and saprotrophic fungi under SP treatment.Among the top 20 metabolism pathways,80%were upregulated in SP treatment compared to the CK.【Conclusions】Seed soaking with beneficial microbial strain promotes the growth of Lanzhou lily bulbs.The beneficial microorganisms play a crucial role in regulating soil microbial structures,enhancing the accumulation of endophytic fungi,reducing the abundance of pathogens,and improving soil functions.Furthermore,specific microbial groups are found to be involved in maintaining soil health.展开更多
该研究利用Illumina Mi Seq测序技术研究高温大曲发酵过程中真菌群落的演替规律。α多样性分析结果表明,高温大曲发酵过程中真菌群落的丰富度和多样性均呈先上升后下降的趋势,在第二次翻曲时,发现物种数(369.16)和辛普森指数(0.75)均达...该研究利用Illumina Mi Seq测序技术研究高温大曲发酵过程中真菌群落的演替规律。α多样性分析结果表明,高温大曲发酵过程中真菌群落的丰富度和多样性均呈先上升后下降的趋势,在第二次翻曲时,发现物种数(369.16)和辛普森指数(0.75)均达到最大,且极显著高于拆曲出库时(P<0.01);优势真菌属包括嗜热子囊菌属(Thermoascus)、嗜热真菌属(Thermomyces)、曲霉属(Aspergillus)、罗萨氏菌属(Rasamsonia)和丝衣霉菌属(Byssochlamys)。β多样性分析结果表明,高温大曲发酵过程中真菌群落结构发生了较大变化。线性判别分析效应值大小(LEfSe)分析结果表明,不同发酵阶段呈现出特征性优势菌,Phialosimplex、Thermoascus和Thermomyces可分别为第一次翻曲、第二次翻曲和拆曲出库阶段的生物标志物。相关性分析结果表明,真菌群落结构的变化可能与菌群间的互作关系密切相关。该研究结果为后续优化大曲发酵过程和提高产品品质奠定了基础。展开更多
基金Supported by the National Natural Science Foundations of China(3127218631301791)
文摘Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.
基金Supported by the Natural Science Fund of Heilongjiang Province(LC2016009)(GH)U.S.Department of Energy and U.S.Department of Agricultural Plant Feedstocks Genomics for Bioenergy Program(DE-SC0008338 to XZ and BZ)。
文摘Switchgrass(Panicum virgatum L.)as a high-quality bioenergy crop that can effectively improve saline-alkali soil has strong resistance to stress and grows well in marginal soil and some abiotic stress environments.This study used alkali-sensitive genotype AM(AM-314/MS-155)and alkali-tolerant genotype ALA(Alamo)as experimental materials to investigate molecular mechanisms of switchgrass tolerance to alkali-salt stress.When the plants were grown to E5 stage,the alkali-salt stress treatment was carried out by soaking method(Na2CO3:NaHCO3=1:9,C(Na+)=150 mmol·L-1 and pH=9.0)and fresh root samples were taken after treatments for 0(CK),6 and 24 h,respectively,the differentially expressed microRNAs and their regulatory network were analyzed.A total of 1049 known miRNAs and 68 novel miRNAs were identified.Seventy-two differentially expressed miRNAs in ALA were more than three times higher than those in AM and 36.1%differentially expressed miRNAs was significantly down-regulated(p<0.05).Through analyses of differentially expressed miRNAs and their target genes,it was found that under alkali-salt stress,differentially expressed miRNAs in AM were mainly involved in the regulation of cellular ROS clearance,ethylene signal transduction,and root,leaf and flower development.MiRNAs in ALA were also involved in water transport,DNA methylation,response to high osmotic pressure,activation of stress-related genes and more complex responses to alkali-salt stress processes,but those in AM were not.ALA was significantly higher than AM in the number of microRNAs responding to alkali-salt stress and in the functional diversity of their regulatory target genes.
文摘【Background】The application of beneficial-microbial seed soaking prior to sowing represents a novel technology that has not been employed in Lanzhou lily cultivation.We conducted an experiment to explore the impact of this soaking method on the fungal and bacterial community structures using next-generation sequencing technology(NGS).【Methods】Lily bulbs were soaked in a seed treating agent containing beneficial microbes(SP treatment)for 4 hours.Subsequently,they were planted in soil in July and sampled in September to assess plant growth,rhizosphere soil physicochemical properties,and microorganism community structures.In addition,we employed the software PICRUSt and FUNGuild to predict bacterial pathways and fungal functions.【Results】Under SP treatment,there were significant alterations in fungi and bacteria community structures,accompanied by improved soil nutrient status.Notably,the relative abundance of dominant microorganism groups,such as the fungi Basidiomycota,Pseudeurotium,Cladophialophora,Microascus,and Dactylonectria,as well as the bacteria Proteobacteria,Chloroflexi,Ochrobactrium,Lysobacter,and RB41,underwent notable changes.Microorganism function prediction results indicated a reduction in pathotrophic fungi(including plant pathogens)and an increase in endophytic and saprotrophic fungi under SP treatment.Among the top 20 metabolism pathways,80%were upregulated in SP treatment compared to the CK.【Conclusions】Seed soaking with beneficial microbial strain promotes the growth of Lanzhou lily bulbs.The beneficial microorganisms play a crucial role in regulating soil microbial structures,enhancing the accumulation of endophytic fungi,reducing the abundance of pathogens,and improving soil functions.Furthermore,specific microbial groups are found to be involved in maintaining soil health.
文摘该研究利用Illumina Mi Seq测序技术研究高温大曲发酵过程中真菌群落的演替规律。α多样性分析结果表明,高温大曲发酵过程中真菌群落的丰富度和多样性均呈先上升后下降的趋势,在第二次翻曲时,发现物种数(369.16)和辛普森指数(0.75)均达到最大,且极显著高于拆曲出库时(P<0.01);优势真菌属包括嗜热子囊菌属(Thermoascus)、嗜热真菌属(Thermomyces)、曲霉属(Aspergillus)、罗萨氏菌属(Rasamsonia)和丝衣霉菌属(Byssochlamys)。β多样性分析结果表明,高温大曲发酵过程中真菌群落结构发生了较大变化。线性判别分析效应值大小(LEfSe)分析结果表明,不同发酵阶段呈现出特征性优势菌,Phialosimplex、Thermoascus和Thermomyces可分别为第一次翻曲、第二次翻曲和拆曲出库阶段的生物标志物。相关性分析结果表明,真菌群落结构的变化可能与菌群间的互作关系密切相关。该研究结果为后续优化大曲发酵过程和提高产品品质奠定了基础。
