Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Sinc...Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Since it was first used to profile single-cell transcriptome in plants in 2019,it has been extensively employed to perform different research in plants.Recently,scRNA-seq was also quickly adopted by the cotton research community to solve lots of scientific questions which have been never solved.In this comment,we highlighted the significant progress in employing scRNA-seq to cotton genetic and genomic study and its future potential applications.展开更多
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
OBJECTIVE o facilitate the basic acquaintance with the bioactive lycodine-type alkaloids biosynthetic pathways,we conducted the transcriptome analysis of L.casuarinoides by illumina sequencing.METHODS The plant of L.c...OBJECTIVE o facilitate the basic acquaintance with the bioactive lycodine-type alkaloids biosynthetic pathways,we conducted the transcriptome analysis of L.casuarinoides by illumina sequencing.METHODS The plant of L.casuarinoides was collected and was subjected to RNA isolation,cDNA library construction,and illumina sequencing before bioinformatics analysis.After sequencing,the clean reads were obtained for de novo assembly by using Trinity software,and then further processed with TGICL sequencing clustering software to generate unigenes,The unigenes are aligned by Blast X alignment to six public protein database.In addition,all unigenes are functionally annotated by GO,KEGG and characterized putative genes involved in lycopodium alkaloids biosynthesis.RESULTS In total,124,524 high-quality unigenes were obtained with an average sequence length of 601 bp.Among the L.casuarinoides transcripts,61,304 showed significant similarity(E-value<1 e-5) to the known proteins in the public database.Among the total 124 524 unigenes,47,538 open reading frame(ORFs) were predicted.Based on the bioinformatics analysis,all possible enzymes involved in the Lycodine-type alkaloids biosynthetic pathway of L.casuarinoides were identified,including primary amine oxidase(PAO),and Malonly-CoA decarboxylase.In addition,a total of 64 putative cytochrome P450(CYP450) and 827 transcription factors were selected as the candidates of Lycodine-type alka.loids modifiers.Furthermore,a total of 13 352 simple sequence repeats(SSRs) were identified from the 124,524 unigenes,of which dinucleotide motifs AG/CT(50.1%),were the most abundant.CONCLU.SION This transcriptome analysis of L.casuarinoides,provides many valuable candidate genes involv.ing in the biosynthesis of novel secondary metabolites but also lays the foundation for genetic diversity analysis via SSRs markers in L.casuarinoides.展开更多
白凤菜含有丰富的矿质元素、氨基酸和锌,在许多地区颇受欢迎,是公认的保健蔬菜,具有一定的药用和食用价值。本研究利用Illumina HiSeq X Ten技术平台对白凤菜进行了转录组测序,并与生化提取、q RT-PCR结果进行交叉验证。结果发现白凤菜...白凤菜含有丰富的矿质元素、氨基酸和锌,在许多地区颇受欢迎,是公认的保健蔬菜,具有一定的药用和食用价值。本研究利用Illumina HiSeq X Ten技术平台对白凤菜进行了转录组测序,并与生化提取、q RT-PCR结果进行交叉验证。结果发现白凤菜一年生长期叶片中的总黄酮含量显著高于半年生长期叶片中的总黄酮含量;转录组结果则显示在一年生长期叶片中,与黄酮生物合成相关的基因中共有10个基因显著上调表达;利用qRT-PCR深入挖掘在总黄酮上调表达路径中的关键基因,发现一年生长期叶片中无色花青素双加氧酶/花青素合成酶(LDOX/ANS)与类黄酮-3’-羟化酶(F3'H)呈显著上调表达。综上,生化提取与转录组数据均显示,一年生长期叶片中总黄酮含量高于半年期叶片,且LDOX/ANS与F3'H在其中起关键调控作用。本研究结果为白凤菜分子生物学研究奠定基础,为白凤菜药用活性成分的生物合成调控、品质改良、品种选育等提供参考依据。展开更多
文摘Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Since it was first used to profile single-cell transcriptome in plants in 2019,it has been extensively employed to perform different research in plants.Recently,scRNA-seq was also quickly adopted by the cotton research community to solve lots of scientific questions which have been never solved.In this comment,we highlighted the significant progress in employing scRNA-seq to cotton genetic and genomic study and its future potential applications.
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 Jiangxi′s Major International Science and Technology Cooperation Projects(20151BDH80020)
文摘OBJECTIVE o facilitate the basic acquaintance with the bioactive lycodine-type alkaloids biosynthetic pathways,we conducted the transcriptome analysis of L.casuarinoides by illumina sequencing.METHODS The plant of L.casuarinoides was collected and was subjected to RNA isolation,cDNA library construction,and illumina sequencing before bioinformatics analysis.After sequencing,the clean reads were obtained for de novo assembly by using Trinity software,and then further processed with TGICL sequencing clustering software to generate unigenes,The unigenes are aligned by Blast X alignment to six public protein database.In addition,all unigenes are functionally annotated by GO,KEGG and characterized putative genes involved in lycopodium alkaloids biosynthesis.RESULTS In total,124,524 high-quality unigenes were obtained with an average sequence length of 601 bp.Among the L.casuarinoides transcripts,61,304 showed significant similarity(E-value<1 e-5) to the known proteins in the public database.Among the total 124 524 unigenes,47,538 open reading frame(ORFs) were predicted.Based on the bioinformatics analysis,all possible enzymes involved in the Lycodine-type alkaloids biosynthetic pathway of L.casuarinoides were identified,including primary amine oxidase(PAO),and Malonly-CoA decarboxylase.In addition,a total of 64 putative cytochrome P450(CYP450) and 827 transcription factors were selected as the candidates of Lycodine-type alka.loids modifiers.Furthermore,a total of 13 352 simple sequence repeats(SSRs) were identified from the 124,524 unigenes,of which dinucleotide motifs AG/CT(50.1%),were the most abundant.CONCLU.SION This transcriptome analysis of L.casuarinoides,provides many valuable candidate genes involv.ing in the biosynthesis of novel secondary metabolites but also lays the foundation for genetic diversity analysis via SSRs markers in L.casuarinoides.
文摘白凤菜含有丰富的矿质元素、氨基酸和锌,在许多地区颇受欢迎,是公认的保健蔬菜,具有一定的药用和食用价值。本研究利用Illumina HiSeq X Ten技术平台对白凤菜进行了转录组测序,并与生化提取、q RT-PCR结果进行交叉验证。结果发现白凤菜一年生长期叶片中的总黄酮含量显著高于半年生长期叶片中的总黄酮含量;转录组结果则显示在一年生长期叶片中,与黄酮生物合成相关的基因中共有10个基因显著上调表达;利用qRT-PCR深入挖掘在总黄酮上调表达路径中的关键基因,发现一年生长期叶片中无色花青素双加氧酶/花青素合成酶(LDOX/ANS)与类黄酮-3’-羟化酶(F3'H)呈显著上调表达。综上,生化提取与转录组数据均显示,一年生长期叶片中总黄酮含量高于半年期叶片,且LDOX/ANS与F3'H在其中起关键调控作用。本研究结果为白凤菜分子生物学研究奠定基础,为白凤菜药用活性成分的生物合成调控、品质改良、品种选育等提供参考依据。
