Drought is one of the most important abiotic stresses affecting maize growth and development and therefore resulting in yield loss.Thus it is essential to understand molecular mechanisms of drought stress responses in...Drought is one of the most important abiotic stresses affecting maize growth and development and therefore resulting in yield loss.Thus it is essential to understand molecular mechanisms of drought stress responses in maize for drought tolerance improvement.The root plays a critical role in plants sensing water deficit.In the present study,two maize inbred lines,H082183,a drought-tolerant line,and Lv28,a drought-sensitive line,were grown in the field and treated with different water conditions(moderate drought,severe drought,and well-watered conditions)during vegetative stage.The transcriptomes of their roots were investigated by RNA sequencing.There were 1428 and 512 drought-responsive genes(DRGs)in Lv28,688 and 3363 DRGs in H082183 under moderate drought and severe drought,respectively.A total of 31 Gene Ontology(GO)terms were significantly over-represented in the two lines,13 of which were enriched only in the DRGs of H082183.Based on results of Kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis,"plant hormone signal transduction"and"starch and sucrose metabolism"were enriched in both of the two lines,while"phenylpropanoid biosynthesis"was only enriched in H082183.Further analysis revealed the different expression patterns of genes related to abscisic acid(ABA)signal pathway,trehalose biosynthesis,reactive oxygen scavenging,and transcription factors might contribute to drought tolerance in maize.Our results contribute to illustrating drought-responsive molecular mechanisms and providing gene resources for maize drought improvement.展开更多
A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN (duplex-specific nuclease) normalization method combined with the SMART (Switching Mechanism At 5' end ...A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN (duplex-specific nuclease) normalization method combined with the SMART (Switching Mechanism At 5' end of the RNA Transcript) technique. The titer of the original cDNA library was about 1.5 × 10^6 cfu·mL^-1 and the average insertion size was about 1 kb with a high recombination rate (97%). The 5011 high-quality expressed sequence tags (ESTs) were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally anno- tated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 (50.1%) unigenes were associated with 4082 Gene Ontology (GO) terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups (COG) functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase (RLK) genes were screened. Furthermore, a total of 94 simple sequence repeats (SSRs) were discovered, of which 20 loci were successfully amplified in C debaoensis. This study is the first EST analysis for the coralloid roots of C debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C debaoensis and related cycad species.展开更多
Maize roots are important component for plant adaptation to soil water deficits because they are supposed to take up water and necessary solutes from the soil. In the present study, the drought-induced genes were isol...Maize roots are important component for plant adaptation to soil water deficits because they are supposed to take up water and necessary solutes from the soil. In the present study, the drought-induced genes were isolated in maize roots. A suppression subtractive hybridization protocol was applied to construct a forward subtractive cDNA library from CN165 for drought-stressed maize roots and a number of drought-induced genes were isolated. Totally, 126 uniESTs (containing 82 singlets and 44 contigs) were obtained from 503 available ESTs sequences after macroarray hybridization. UniESTs were analyzed using BLASTN and BLASTX and the results showed that 92% of the uniESTs had homolgous sequences in maize nr database by BLASTN. About 89% of uniESTs appeared the homlogous amino acid sequences in rice protein database but not in maize protein database by BLASTX, implying that those genes are likely new functional genes in maize. Function analysis showed that those genes were involved in a broad spectrum of biological pathways, mainly in signaling and regulatory pathways related to stress tolerance.展开更多
Japanese Angelica Root prepared from Angelica acutiloba var. acutiloba and A. acutiloba var. sugiyamae, known in Japan as “Toki” and “Hokkai Toki”, is an important crude drug used in Kampo medicine (traditional Ja...Japanese Angelica Root prepared from Angelica acutiloba var. acutiloba and A. acutiloba var. sugiyamae, known in Japan as “Toki” and “Hokkai Toki”, is an important crude drug used in Kampo medicine (traditional Japanese medicine). However, since these Angelica varieties have recently outcrossed with each other, it is unclear whether Japanese Angelica Root sold for use in Kampo medicine is a pure variety. Here, we describe DNA sequence polymorphisms that can be used to distinguish between A. acutiloba var. acutiloba and A. acutiloba var. sugiyamae. In our analyses, differences in the trnK region of chloroplast DNA distinguished among some A. acutiloba varieties and related species, but not between A. acutiloba var. acutiloba and A. acutiloba var. iwatensis. One geographical strain of A. acutiloba var. acutiloba and A. acutiloba var. sugiyamae showed identical sequences in three regions of chloroplast DNA, but differences in the internal transcribed spacer region of nuclear ribosomal DNA. One strain of A. acutiloba var. iwatensis and A. acutiloba var. sugiyamae had identical sequences in all of the chloroplast and nuclear ribosomal DNA regions examined. These findings show that A. acutiloba var. acutiloba has hybridized with A. acutiloba var. sugiyamae and that the “Hokkai Toki” variety resulted from outcrossing with A. acutiloba var. iwatensis. Molecular authentication based on analyses of chloroplast and nuclear ribosomal DNA sequences of A. acutiloba and related species is an efficient method to authenticate Japanese Angelica Root at the variety level. Therefore, these analyses can determine whether a product is derived from A. acutiloba var. acutiloba or A. acutiloba var. sugiyamae.展开更多
The root system is fundamental for maize growth and yield.Characterizing its heterogeneity and cell type-specific response to nitrate at the single-cell level will shed light on root development and nutrient uptake.We...The root system is fundamental for maize growth and yield.Characterizing its heterogeneity and cell type-specific response to nitrate at the single-cell level will shed light on root development and nutrient uptake.We profiled the transcriptomes of>7000 cells derived from root tips of maize seedlings grown on media with or without nitrate,and identified 11 major cell types or tissues and 85 cell type-specific nitrate-response genes,including several known nitrate metabolic genes.A pseudotime analysis showed a continuous pseudotime series with the beginning at meristematic zone cells and showed that the root hair cell was derived by differentiation of a subset of epidermal cells.Interspecies comparison of root cells between maize and rice revealed the conservation and divergence of the root cell types and identified 57,216,and 80 conserved orthologous genes in root hair,endodermis,and phloem cells respectively.This study provides a global view of maize root tip developmental processes and responses to nitrate at the single-cell level.The genes described in the present work could serve as targets for further genetic analyses and accurate regulation of gene expression and phenotypic variation in specific cell types or tissues.展开更多
The regenerative capacity of peripheral nerves is limited after nerve injury.A number of growth factors modulate many cellular behaviors,such as proliferation and migration,and may contribute to nerve repair and regen...The regenerative capacity of peripheral nerves is limited after nerve injury.A number of growth factors modulate many cellular behaviors,such as proliferation and migration,and may contribute to nerve repair and regeneration.Our previous study observed the dynamic changes of genes in L4–6 dorsal root ganglion after rat sciatic nerve crush using transcriptome sequencing.Our current study focused on upstream growth factors and found that a total of 19 upstream growth factors were dysregulated in dorsal root ganglions at 3,9 hours,1,4,or 7 days after nerve crush,compared with the 0 hour control.Thirty-six rat models of sciatic nerve crush injury were prepared as described previously.Then,they were divided into six groups to measure the expression changes of representative genes at 0,3,9 hours,1,4 or 7 days post crush.Our current study measured the expression levels of representative upstream growth factors,including nerve growth factor,brain-derived neurotrophic factor,fibroblast growth factor 2 and amphiregulin genes,and explored critical signaling pathways and biological process through bioinformatic analysis.Our data revealed that many of these dysregulated upstream growth factors,including nerve growth factor,brain-derived neurotrophic factor,fibroblast growth factor 2 and amphiregulin,participated in tissue remodeling and axon growth-related biological processes Therefore,the experiment described the expression pattern of upstream growth factors in the dorsal root ganglia after peripheral nerve injury.Bioinformatic analysis revealed growth factors that may promote repair and regeneration of damaged peripheral nerves.All animal surgery procedures were performed in accordance with Institutional Animal Care Guidelines of Nantong University and ethically approved by the Administration Committee of Experimental Animals,China(approval No.20170302-017)on March 2,2017.展开更多
Plant growth promontory Pseudomonas strains were isolated from root nodules of five plant species, viz., Trifolium pretense, Cicer arietinum, Amaranthus polygamus, Vigna mungo, and Trigonella foenum;that plants were d...Plant growth promontory Pseudomonas strains were isolated from root nodules of five plant species, viz., Trifolium pretense, Cicer arietinum, Amaranthus polygamus, Vigna mungo, and Trigonella foenum;that plants were denizen of Shekhawati region of Rajasthan. A total of 8 bacterial isolates were evaluated for growth promotion using PGP properties. Partial 16S rDNA sequencing data showed that these 8 bacterial isolates belonged to genus Pseudomonas. MEGA 4.0.2, software was used to construct a neighbor joining tree by employing boot strap method. Result exhibited significant diversity among recovered Pseudomonas strains.展开更多
在全球气候变化和高强度人类活动的共同影响下,许多流域天然水循环过程受到破坏。径流序列呈现明显的非平稳特性,给水资源规划、管理、预测和调控带来一定的挑战。揭示径流序列的非平稳特性可以有效应对全球气候变化下的复杂水问题,对...在全球气候变化和高强度人类活动的共同影响下,许多流域天然水循环过程受到破坏。径流序列呈现明显的非平稳特性,给水资源规划、管理、预测和调控带来一定的挑战。揭示径流序列的非平稳特性可以有效应对全球气候变化下的复杂水问题,对降低水文分析难度和提高径流预测精度具有十分重要的意义。研究以汾河上游兰村站为研究对象,分析该站1958-2016年年径流和月径流序列是否平稳。首先从随机水文学角度,采用Mann-Kendall检验法和小波分析法识别径流序列的趋势、突变和周期特征。在此基础上,从统计水文学角度引入Ng-Perron单位根检验方法。通过Mann-Kendall趋势检验和散点图法选择合适的检验方程,对径流序列进行广义最小二乘法(Generalized Least Squares,GLS)退势,并利用修正的信息准则(Modified information criterion,MIC)计算最优时间滞后阶数,判别径流序列是否具有非平稳性。结果显示,径流序列存在趋势、突变和周期成分,为非平稳径流序列。同时Ng-Perron单位根检验表明,该站年、月径流序列在1%显著性水平上具有非平稳特性。相较传统单位根检验方法,Ng-Perron单位根检验采用更为稳健的修正检验统计量,显著调整小样本情况下水平扭曲的现象,具有更好检验水平和功效,因而可以得到更合理的检验结果。研究成果为径流序列非平稳性检验理论的进一步改进及径流预测模型发展与应用提供参考。展开更多
基金supported by the Sci-Tech Innovation Program of Chinese Academy of Agricultural Sciences (Y2016PT10)
文摘Drought is one of the most important abiotic stresses affecting maize growth and development and therefore resulting in yield loss.Thus it is essential to understand molecular mechanisms of drought stress responses in maize for drought tolerance improvement.The root plays a critical role in plants sensing water deficit.In the present study,two maize inbred lines,H082183,a drought-tolerant line,and Lv28,a drought-sensitive line,were grown in the field and treated with different water conditions(moderate drought,severe drought,and well-watered conditions)during vegetative stage.The transcriptomes of their roots were investigated by RNA sequencing.There were 1428 and 512 drought-responsive genes(DRGs)in Lv28,688 and 3363 DRGs in H082183 under moderate drought and severe drought,respectively.A total of 31 Gene Ontology(GO)terms were significantly over-represented in the two lines,13 of which were enriched only in the DRGs of H082183.Based on results of Kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis,"plant hormone signal transduction"and"starch and sucrose metabolism"were enriched in both of the two lines,while"phenylpropanoid biosynthesis"was only enriched in H082183.Further analysis revealed the different expression patterns of genes related to abscisic acid(ABA)signal pathway,trehalose biosynthesis,reactive oxygen scavenging,and transcription factors might contribute to drought tolerance in maize.Our results contribute to illustrating drought-responsive molecular mechanisms and providing gene resources for maize drought improvement.
基金supported by the Grant(201522)from Shenzhen Urban Management
文摘A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN (duplex-specific nuclease) normalization method combined with the SMART (Switching Mechanism At 5' end of the RNA Transcript) technique. The titer of the original cDNA library was about 1.5 × 10^6 cfu·mL^-1 and the average insertion size was about 1 kb with a high recombination rate (97%). The 5011 high-quality expressed sequence tags (ESTs) were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally anno- tated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 (50.1%) unigenes were associated with 4082 Gene Ontology (GO) terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups (COG) functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase (RLK) genes were screened. Furthermore, a total of 94 simple sequence repeats (SSRs) were discovered, of which 20 loci were successfully amplified in C debaoensis. This study is the first EST analysis for the coralloid roots of C debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C debaoensis and related cycad species.
基金The research was supported bythe National Natural Science Foundation of China(30730063) 973 Program of China (2006CB101700)the National Technology R&D Program of China(2006BAD13B03).
文摘Maize roots are important component for plant adaptation to soil water deficits because they are supposed to take up water and necessary solutes from the soil. In the present study, the drought-induced genes were isolated in maize roots. A suppression subtractive hybridization protocol was applied to construct a forward subtractive cDNA library from CN165 for drought-stressed maize roots and a number of drought-induced genes were isolated. Totally, 126 uniESTs (containing 82 singlets and 44 contigs) were obtained from 503 available ESTs sequences after macroarray hybridization. UniESTs were analyzed using BLASTN and BLASTX and the results showed that 92% of the uniESTs had homolgous sequences in maize nr database by BLASTN. About 89% of uniESTs appeared the homlogous amino acid sequences in rice protein database but not in maize protein database by BLASTX, implying that those genes are likely new functional genes in maize. Function analysis showed that those genes were involved in a broad spectrum of biological pathways, mainly in signaling and regulatory pathways related to stress tolerance.
文摘Japanese Angelica Root prepared from Angelica acutiloba var. acutiloba and A. acutiloba var. sugiyamae, known in Japan as “Toki” and “Hokkai Toki”, is an important crude drug used in Kampo medicine (traditional Japanese medicine). However, since these Angelica varieties have recently outcrossed with each other, it is unclear whether Japanese Angelica Root sold for use in Kampo medicine is a pure variety. Here, we describe DNA sequence polymorphisms that can be used to distinguish between A. acutiloba var. acutiloba and A. acutiloba var. sugiyamae. In our analyses, differences in the trnK region of chloroplast DNA distinguished among some A. acutiloba varieties and related species, but not between A. acutiloba var. acutiloba and A. acutiloba var. iwatensis. One geographical strain of A. acutiloba var. acutiloba and A. acutiloba var. sugiyamae showed identical sequences in three regions of chloroplast DNA, but differences in the internal transcribed spacer region of nuclear ribosomal DNA. One strain of A. acutiloba var. iwatensis and A. acutiloba var. sugiyamae had identical sequences in all of the chloroplast and nuclear ribosomal DNA regions examined. These findings show that A. acutiloba var. acutiloba has hybridized with A. acutiloba var. sugiyamae and that the “Hokkai Toki” variety resulted from outcrossing with A. acutiloba var. iwatensis. Molecular authentication based on analyses of chloroplast and nuclear ribosomal DNA sequences of A. acutiloba and related species is an efficient method to authenticate Japanese Angelica Root at the variety level. Therefore, these analyses can determine whether a product is derived from A. acutiloba var. acutiloba or A. acutiloba var. sugiyamae.
基金financially supported by the Special Project of Guangdong Academy of Sciences,China(2020GDASYL-20200103073)the Special Project for Research and Development in Key areas of Guangdong Province(2019B020238001)the National Natural Science Foundation of China(32072027)。
文摘The root system is fundamental for maize growth and yield.Characterizing its heterogeneity and cell type-specific response to nitrate at the single-cell level will shed light on root development and nutrient uptake.We profiled the transcriptomes of>7000 cells derived from root tips of maize seedlings grown on media with or without nitrate,and identified 11 major cell types or tissues and 85 cell type-specific nitrate-response genes,including several known nitrate metabolic genes.A pseudotime analysis showed a continuous pseudotime series with the beginning at meristematic zone cells and showed that the root hair cell was derived by differentiation of a subset of epidermal cells.Interspecies comparison of root cells between maize and rice revealed the conservation and divergence of the root cell types and identified 57,216,and 80 conserved orthologous genes in root hair,endodermis,and phloem cells respectively.This study provides a global view of maize root tip developmental processes and responses to nitrate at the single-cell level.The genes described in the present work could serve as targets for further genetic analyses and accurate regulation of gene expression and phenotypic variation in specific cell types or tissues.
基金supported by the Natural Science Foundation of Jiangsu Higher Education Institutions of China(Major Program),No.16KJA310005(to SYL)the Natural Science Foundation of Nantong City of China,No.JC2018058(to TMQ)the Priority Academic Program Development of Jiangsu Higher Education Institutions of China
文摘The regenerative capacity of peripheral nerves is limited after nerve injury.A number of growth factors modulate many cellular behaviors,such as proliferation and migration,and may contribute to nerve repair and regeneration.Our previous study observed the dynamic changes of genes in L4–6 dorsal root ganglion after rat sciatic nerve crush using transcriptome sequencing.Our current study focused on upstream growth factors and found that a total of 19 upstream growth factors were dysregulated in dorsal root ganglions at 3,9 hours,1,4,or 7 days after nerve crush,compared with the 0 hour control.Thirty-six rat models of sciatic nerve crush injury were prepared as described previously.Then,they were divided into six groups to measure the expression changes of representative genes at 0,3,9 hours,1,4 or 7 days post crush.Our current study measured the expression levels of representative upstream growth factors,including nerve growth factor,brain-derived neurotrophic factor,fibroblast growth factor 2 and amphiregulin genes,and explored critical signaling pathways and biological process through bioinformatic analysis.Our data revealed that many of these dysregulated upstream growth factors,including nerve growth factor,brain-derived neurotrophic factor,fibroblast growth factor 2 and amphiregulin,participated in tissue remodeling and axon growth-related biological processes Therefore,the experiment described the expression pattern of upstream growth factors in the dorsal root ganglia after peripheral nerve injury.Bioinformatic analysis revealed growth factors that may promote repair and regeneration of damaged peripheral nerves.All animal surgery procedures were performed in accordance with Institutional Animal Care Guidelines of Nantong University and ethically approved by the Administration Committee of Experimental Animals,China(approval No.20170302-017)on March 2,2017.
文摘Plant growth promontory Pseudomonas strains were isolated from root nodules of five plant species, viz., Trifolium pretense, Cicer arietinum, Amaranthus polygamus, Vigna mungo, and Trigonella foenum;that plants were denizen of Shekhawati region of Rajasthan. A total of 8 bacterial isolates were evaluated for growth promotion using PGP properties. Partial 16S rDNA sequencing data showed that these 8 bacterial isolates belonged to genus Pseudomonas. MEGA 4.0.2, software was used to construct a neighbor joining tree by employing boot strap method. Result exhibited significant diversity among recovered Pseudomonas strains.
文摘在全球气候变化和高强度人类活动的共同影响下,许多流域天然水循环过程受到破坏。径流序列呈现明显的非平稳特性,给水资源规划、管理、预测和调控带来一定的挑战。揭示径流序列的非平稳特性可以有效应对全球气候变化下的复杂水问题,对降低水文分析难度和提高径流预测精度具有十分重要的意义。研究以汾河上游兰村站为研究对象,分析该站1958-2016年年径流和月径流序列是否平稳。首先从随机水文学角度,采用Mann-Kendall检验法和小波分析法识别径流序列的趋势、突变和周期特征。在此基础上,从统计水文学角度引入Ng-Perron单位根检验方法。通过Mann-Kendall趋势检验和散点图法选择合适的检验方程,对径流序列进行广义最小二乘法(Generalized Least Squares,GLS)退势,并利用修正的信息准则(Modified information criterion,MIC)计算最优时间滞后阶数,判别径流序列是否具有非平稳性。结果显示,径流序列存在趋势、突变和周期成分,为非平稳径流序列。同时Ng-Perron单位根检验表明,该站年、月径流序列在1%显著性水平上具有非平稳特性。相较传统单位根检验方法,Ng-Perron单位根检验采用更为稳健的修正检验统计量,显著调整小样本情况下水平扭曲的现象,具有更好检验水平和功效,因而可以得到更合理的检验结果。研究成果为径流序列非平稳性检验理论的进一步改进及径流预测模型发展与应用提供参考。