Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function.Although the availability of massive RNA-seq data provi...Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function.Although the availability of massive RNA-seq data provides great opportunities for gene model refinement,few efforts have been made to adopt these precious data in rice genome reannotation.Here we reannotate the rice(Oryza sativa L.ssp.japonica)genome based on integration of large-scale RNA-seq data and release a new annotation system IC4 R-2.0.In general,IC4 R-2.0 significantly improves the completeness of gene structure,identifies a number of novel genes,and integrates a variety of functional annotations.Furthermore,long non-coding RNAs(lncRNAs)and circular RNAs(circRNAs)are systematically characterized in the rice genome.Performance evaluation shows that compared to previous annotation systems,IC4 R-2.0 achieves higher integrity and quality,primarily attributable to massive RNA-seq data applied in genome annotation.Consequently,we incorporate the improved annotations into the Information Commons for Rice(IC4 R),a database integrating multiple omics data of rice,and accordingly update IC4 R by providing more user-friendly web interfaces and implementing a series of practical online tools.Together,the updated IC4 R,which is equipped with the improved annotations,bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species.The IC4 R-2.0 annotation system and related resources are freely accessible at http://ic4 r.org/.展开更多
The original gas reservoirs in different areas and different layers of the Triassic Xujiahe Formation in the central Sichuan Basin are studied to reveal the relationships of iC4/nC4 and iC5/nC5 ratios in coal-derived ...The original gas reservoirs in different areas and different layers of the Triassic Xujiahe Formation in the central Sichuan Basin are studied to reveal the relationships of iC4/nC4 and iC5/nC5 ratios in coal-derived gas components with maturity using conventional natural gas geochemical research methods. The testing results of 73 gas samples from 8 gas fields show that the iC4/nC4 and iC5/nC5 ratios in coal-derived gas have a good positive correlation, and the correlation coefficient is above 0.8. Both the iC4/nC4 and iC5/nC5 ratios become higher with the increase of natural gas dryness coefficient (C1/C1+) and the methane carbon isotope becoming less negative. These parameters are highly correlated. This study not only reveals characteristics of heavy hydrocarbon isomers generated by coal formation, but also puts forward new identification indicators reflecting the maturity of coal-derived gas, the regression between iC4/nC4, iC5/nC5 and Ro, which can provide an important reference for maturity, migration and accumulation of coal-derived gas, and late stage reformation of coal-derived gas reservoirs.展开更多
基金supported by grants from the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDA08020102 to ZZ and SH)the Youth Innovation Promotion Association of Chinese Academy of Science(Grant No.2018134 to LH)+2 种基金National Programs for High TechnologyResearch and Development(Grant Nos.2015AA020108 and 2012AA020409 to ZZ)the 100-Talent Program of Chinese Academy of Sciences(to YB and ZZ)the National Natural Science Foundation of China(Grant No.31100915 to LH)
文摘Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function.Although the availability of massive RNA-seq data provides great opportunities for gene model refinement,few efforts have been made to adopt these precious data in rice genome reannotation.Here we reannotate the rice(Oryza sativa L.ssp.japonica)genome based on integration of large-scale RNA-seq data and release a new annotation system IC4 R-2.0.In general,IC4 R-2.0 significantly improves the completeness of gene structure,identifies a number of novel genes,and integrates a variety of functional annotations.Furthermore,long non-coding RNAs(lncRNAs)and circular RNAs(circRNAs)are systematically characterized in the rice genome.Performance evaluation shows that compared to previous annotation systems,IC4 R-2.0 achieves higher integrity and quality,primarily attributable to massive RNA-seq data applied in genome annotation.Consequently,we incorporate the improved annotations into the Information Commons for Rice(IC4 R),a database integrating multiple omics data of rice,and accordingly update IC4 R by providing more user-friendly web interfaces and implementing a series of practical online tools.Together,the updated IC4 R,which is equipped with the improved annotations,bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species.The IC4 R-2.0 annotation system and related resources are freely accessible at http://ic4 r.org/.
基金Supported by the National Natural Science Foundation of China(41872162)
文摘The original gas reservoirs in different areas and different layers of the Triassic Xujiahe Formation in the central Sichuan Basin are studied to reveal the relationships of iC4/nC4 and iC5/nC5 ratios in coal-derived gas components with maturity using conventional natural gas geochemical research methods. The testing results of 73 gas samples from 8 gas fields show that the iC4/nC4 and iC5/nC5 ratios in coal-derived gas have a good positive correlation, and the correlation coefficient is above 0.8. Both the iC4/nC4 and iC5/nC5 ratios become higher with the increase of natural gas dryness coefficient (C1/C1+) and the methane carbon isotope becoming less negative. These parameters are highly correlated. This study not only reveals characteristics of heavy hydrocarbon isomers generated by coal formation, but also puts forward new identification indicators reflecting the maturity of coal-derived gas, the regression between iC4/nC4, iC5/nC5 and Ro, which can provide an important reference for maturity, migration and accumulation of coal-derived gas, and late stage reformation of coal-derived gas reservoirs.