Dear Editor,Over the past decade,significant progress has been made in generating omics data,with genomics as a prime example.In plant sciences,high-quality chromosome-level genomes have been published for over 1000 s...Dear Editor,Over the past decade,significant progress has been made in generating omics data,with genomics as a prime example.In plant sciences,high-quality chromosome-level genomes have been published for over 1000 species(Liu et al.,2024).展开更多
Comparative metabolomics plays a crucial role in investigating gene function,exploring metabolite evolution,and accelerating crop genetic improvement.However,a systematic platform for intra-and crossspecies comparison...Comparative metabolomics plays a crucial role in investigating gene function,exploring metabolite evolution,and accelerating crop genetic improvement.However,a systematic platform for intra-and crossspecies comparison of metabolites is currently lacking.Here,we report the Plant Comparative Metabolome Database(PCMD;http://yanglab.hzau.edu.cn/PCMD),a multilevel comparison database based on predicted metabolic profiles of 530 plant species.The PCMD serves as a platform for comparing metabolite characteristics at various levels,including species,metabolites,pathways,and biological taxonomy.The database also provides a number of user-friendly online tools,such as species comparison,metabolite enrichment,and ID conversion,enabling users to perform comparisons and enrichment analyses of metabolites across different species.In addition,the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite numbering.The PCMD is the most speciesrich comparative plant metabolomics database currently available,and a case study demonstrates its ability to provide new insights into plant metabolic diversity.展开更多
Plant cytochrome P450s play key roles in the diversification and functional modification of plant natural products.Although over 200,000 plant P450 gene sequences have been recorded,only seven crystalized P450 genes s...Plant cytochrome P450s play key roles in the diversification and functional modification of plant natural products.Although over 200,000 plant P450 gene sequences have been recorded,only seven crystalized P450 genes severely hampered the functional characterization,gene mining and engineering of important P450s.Here,we combined Rosetta homologous modeling and MD-based refinement to construct a high-resolution P450 structure prediction process(PCPCM),which was applied to 181 plant P450s with identified functions.Furthermore,we constructed a ligand docking process(PCPLD)that can be applied for plant P450s virtual screening.10 examples of virtual screening indicated the process can reduce about 80%screening space for next experimental verification.Finally,we constructed a plant P450 database(PCPD:http://p450.biodesign.ac.cn/),which includes the sequences,structures and functions of the 181 plant P450s,and a web service based on PCPCM and PCPLD.Our study not only developed methods for the P450-specific structure analysis,but also introduced a universal approach that can assist the mining and functional analysis of P450 enzymes.展开更多
基金supported by the STI 2030-Major Project(2023ZD04069)the Major Science and Technology Research Projects of Guangdong Laboratory for Lingnan Modern Agriculture(NT2021001)+3 种基金the National Natural Science Foundation of China(32400512,32472129,and U24A20392)the Guangdong Basic and Applied Basic Research Foundation(2024A1515011981)the"YouGu"Plan and"Outstanding Youth-Researcher"Program of the Rice Research Institute of Guangdong Academy of Agricultural Sciences(2023YG04&2024YG01)the Introduction of Young Key Talents Program of the Guangdong Academy of Agricultural Sciences(R2023YJ-QC001).
文摘Dear Editor,Over the past decade,significant progress has been made in generating omics data,with genomics as a prime example.In plant sciences,high-quality chromosome-level genomes have been published for over 1000 species(Liu et al.,2024).
基金supported by the National Natural Science Foundation of China(32322061 and 32070559)the Fundamental Research Funds for the Central University HZAU(2662022XXYJ007 and 2662023XX PY001)the China Postdoctoral Science Foundation(2024M751038)。
文摘Comparative metabolomics plays a crucial role in investigating gene function,exploring metabolite evolution,and accelerating crop genetic improvement.However,a systematic platform for intra-and crossspecies comparison of metabolites is currently lacking.Here,we report the Plant Comparative Metabolome Database(PCMD;http://yanglab.hzau.edu.cn/PCMD),a multilevel comparison database based on predicted metabolic profiles of 530 plant species.The PCMD serves as a platform for comparing metabolite characteristics at various levels,including species,metabolites,pathways,and biological taxonomy.The database also provides a number of user-friendly online tools,such as species comparison,metabolite enrichment,and ID conversion,enabling users to perform comparisons and enrichment analyses of metabolites across different species.In addition,the PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite numbering.The PCMD is the most speciesrich comparative plant metabolomics database currently available,and a case study demonstrates its ability to provide new insights into plant metabolic diversity.
基金supported by grants from the National Key R&D Program of China(2020YFC1316400 and No.2019YFA0905700)the National Natural Science Foundation of China(NSFC,Grant Nr.31670100)+1 种基金as well as grants by the NSFC(81560621)the National Science Fund for Excellent Young Scholars(31922047).
文摘Plant cytochrome P450s play key roles in the diversification and functional modification of plant natural products.Although over 200,000 plant P450 gene sequences have been recorded,only seven crystalized P450 genes severely hampered the functional characterization,gene mining and engineering of important P450s.Here,we combined Rosetta homologous modeling and MD-based refinement to construct a high-resolution P450 structure prediction process(PCPCM),which was applied to 181 plant P450s with identified functions.Furthermore,we constructed a ligand docking process(PCPLD)that can be applied for plant P450s virtual screening.10 examples of virtual screening indicated the process can reduce about 80%screening space for next experimental verification.Finally,we constructed a plant P450 database(PCPD:http://p450.biodesign.ac.cn/),which includes the sequences,structures and functions of the 181 plant P450s,and a web service based on PCPCM and PCPLD.Our study not only developed methods for the P450-specific structure analysis,but also introduced a universal approach that can assist the mining and functional analysis of P450 enzymes.
