以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragme...以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragments per kilobase of transcript per million fragments mapped)法计算基因的表达水平,用GO和KEGG数据库对差异表达基因(Differentially expressed genes,DEGs)进行功能注释、富集和代谢通路分析。结果表明,在水稻幼穗发育的早、中、后3个时期分别获得3618个、4183个和5254个差异表达基因,共有4374个差异表达基因得到基因本体(Gene ontology,GO)功能注释,主要涉及DNA结合、细胞进程、信号转导、细胞增殖、物质转运等方面。KEGG数据库分析结果显示,差异表达基因共涉及119条代谢通路,主要包括淀粉和蔗糖代谢通路、内质网中的蛋白质加工通路、激素信号转导通路、细胞周期蛋白通路等。展开更多
Genes controlling fruit appearance determine fruit shape and size. In ethylmethane sulfonate （EMS）-mutagenized lines of Fragaria vesca accession Yellow Wonder （YW）, two fruit shapes are observed： wild-type long f...Genes controlling fruit appearance determine fruit shape and size. In ethylmethane sulfonate （EMS）-mutagenized lines of Fragaria vesca accession Yellow Wonder （YW）, two fruit shapes are observed： wild-type long fruit and mutated shortened fruit （sf）. In this study, we first characterized sf based on morphology, histology, cytology and physiology. The sf was identified as a gibberellin （GA）-deficient mutant, and four complementary DNA （cDNA） libraries separately constructed from flower buds and small green fruits of YW and sfwere sequenced to comparatively analyze transcriptome differences. A total of 29 differentially expressed GA pathway genes were identified by comparisons between YWl and sfl, and 28 differentially expressed GA pathway genes were identified between YW2 and sf2. In addition, the expression patterns of 45 differentially expressed genes were validated by quantificational real-time PCR （qRT-PCR）, and the results were highly concordant with the RNA-Seq results.＇ This transcriptome analysis provides valuable information for understanding the molecular mechanisms of fruit development of strawberry.展开更多
水稻是我国最重要的粮食作物之一,株高和粒型是决定水稻产量的重要因素。通过挖掘水稻株高和粒型调控基因,阐明株高和粒型的调控机制对提高水稻产量的重要意义。在水稻品种吉大718的EMS诱变突变体后代中,筛选出一株矮秆小粒突变体,命名...水稻是我国最重要的粮食作物之一,株高和粒型是决定水稻产量的重要因素。通过挖掘水稻株高和粒型调控基因,阐明株高和粒型的调控机制对提高水稻产量的重要意义。在水稻品种吉大718的EMS诱变突变体后代中,筛选出一株矮秆小粒突变体,命名为dwarf and small grain-JD718(dsg-j)。与野生型吉大718相比,突变体株高变矮,籽粒变小,千粒重下降。通过茎秆第一节间切片观察证实,突变体矮化表型是由细胞变小所致。遗传分析表明,突变体的表型由隐性单基因控制。进一步利用BSA-Seq分析技术将突变体dsg-j基因初步定位在第7染色体。本研究为dsg-j基因的克隆及功能分析奠定了基础,为进一步揭示株高和粒型调控的分子机制提供线索。展开更多
As more information is gathered on the mechanisms of transcription and translation, it is becoming apparent that these processes are highly regulated. The formation of mRNA secondary and tertiary structures is one suc...As more information is gathered on the mechanisms of transcription and translation, it is becoming apparent that these processes are highly regulated. The formation of mRNA secondary and tertiary structures is one such regulatory process that until recently it has not been analysed in depth. Formation of these mRNA structures has the potential to enhance and inhibit alternative splicing of transcripts, and regulate rates and amount of translation. As this regulatory mechanism potentially impacts at both the transcriptional and translational level, while also potentially utilising the vast array of non-coding RNAs, it warrants further investigation. Currently, a variety of high- throughput sequencing techniques including parallel analysis of RNA structure （PARS）, fragmentation sequencing （FragSeq） and selective 2-hydroxyl acylation analysed by primer extension （SHAPE） lead the way in the genome-wide identification and analysis of mRNA structure formation. These new sequencing techniques highlight the diversity and complexity of the transcriptome, and demonstrate another regulatory mechanism that could become a target for new therapeutic approaches.展开更多
Background： Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profilin...Background： Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transeriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data. Results： We review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy. Conclusions： To keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.展开更多
文摘以特大粒水稻品系TD70和小粒籼稻品种Kasalath不同发育时期的幼穗为材料,进行转录组测序。将获得的干净读长(Clean read)以日本晴(Nipponbare)基因组序列为参考序列进行比对得到唯一读长(即特异比对到参考基因组的read),利用FPKM(Fragments per kilobase of transcript per million fragments mapped)法计算基因的表达水平,用GO和KEGG数据库对差异表达基因(Differentially expressed genes,DEGs)进行功能注释、富集和代谢通路分析。结果表明,在水稻幼穗发育的早、中、后3个时期分别获得3618个、4183个和5254个差异表达基因,共有4374个差异表达基因得到基因本体(Gene ontology,GO)功能注释,主要涉及DNA结合、细胞进程、信号转导、细胞增殖、物质转运等方面。KEGG数据库分析结果显示,差异表达基因共涉及119条代谢通路,主要包括淀粉和蔗糖代谢通路、内质网中的蛋白质加工通路、激素信号转导通路、细胞周期蛋白通路等。
基金supported by the National Natural Science Foundation of China(31372037)
文摘Genes controlling fruit appearance determine fruit shape and size. In ethylmethane sulfonate （EMS）-mutagenized lines of Fragaria vesca accession Yellow Wonder （YW）, two fruit shapes are observed： wild-type long fruit and mutated shortened fruit （sf）. In this study, we first characterized sf based on morphology, histology, cytology and physiology. The sf was identified as a gibberellin （GA）-deficient mutant, and four complementary DNA （cDNA） libraries separately constructed from flower buds and small green fruits of YW and sfwere sequenced to comparatively analyze transcriptome differences. A total of 29 differentially expressed GA pathway genes were identified by comparisons between YWl and sfl, and 28 differentially expressed GA pathway genes were identified between YW2 and sf2. In addition, the expression patterns of 45 differentially expressed genes were validated by quantificational real-time PCR （qRT-PCR）, and the results were highly concordant with the RNA-Seq results.＇ This transcriptome analysis provides valuable information for understanding the molecular mechanisms of fruit development of strawberry.
文摘水稻是我国最重要的粮食作物之一,株高和粒型是决定水稻产量的重要因素。通过挖掘水稻株高和粒型调控基因,阐明株高和粒型的调控机制对提高水稻产量的重要意义。在水稻品种吉大718的EMS诱变突变体后代中,筛选出一株矮秆小粒突变体,命名为dwarf and small grain-JD718(dsg-j)。与野生型吉大718相比,突变体株高变矮,籽粒变小,千粒重下降。通过茎秆第一节间切片观察证实,突变体矮化表型是由细胞变小所致。遗传分析表明,突变体的表型由隐性单基因控制。进一步利用BSA-Seq分析技术将突变体dsg-j基因初步定位在第7染色体。本研究为dsg-j基因的克隆及功能分析奠定了基础,为进一步揭示株高和粒型调控的分子机制提供线索。
文摘As more information is gathered on the mechanisms of transcription and translation, it is becoming apparent that these processes are highly regulated. The formation of mRNA secondary and tertiary structures is one such regulatory process that until recently it has not been analysed in depth. Formation of these mRNA structures has the potential to enhance and inhibit alternative splicing of transcripts, and regulate rates and amount of translation. As this regulatory mechanism potentially impacts at both the transcriptional and translational level, while also potentially utilising the vast array of non-coding RNAs, it warrants further investigation. Currently, a variety of high- throughput sequencing techniques including parallel analysis of RNA structure （PARS）, fragmentation sequencing （FragSeq） and selective 2-hydroxyl acylation analysed by primer extension （SHAPE） lead the way in the genome-wide identification and analysis of mRNA structure formation. These new sequencing techniques highlight the diversity and complexity of the transcriptome, and demonstrate another regulatory mechanism that could become a target for new therapeutic approaches.
文摘Background： Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transeriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data. Results： We review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy. Conclusions： To keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.
