MicroTom has a short growth cycle and high transformation efficiency,and is a prospective model plant for studying organ development,metabolism,and plant–microbe interactions.Here,with a newly assembled reference gen...MicroTom has a short growth cycle and high transformation efficiency,and is a prospective model plant for studying organ development,metabolism,and plant–microbe interactions.Here,with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments,we constructed multiple gene co-expression networks,which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth,e.g.arbuscular mycorrhizal symbiosis and fruit development.Additionally,non-coding RNAs,including miRNAs,lncRNAs,and circRNAs were also identified,together with their potential targets.Interacting networks between different types of non-coding RNAs(miRNA-lncRNA),and non-coding RNAs and genes(miRNA-mRNA and lncRNA-mRNA)were constructed as well.Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit.Lastly,we established a database(http://eplant.njau.edu.cn/microTomBase/)with genomic and transcriptomic data,as well as details of gene co-expression and interacting networks on MicroTom,and this database should be of great value to those who want to adopt MicroTom as a model plant for research.展开更多
Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identi...Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identification of a newly discovered hydroxycinnamoyl tyramine(HT) gene cluster in rice.This cluster contains a pyridoxamine 50-phosphate oxidase(Os PDX3) producing the cofactor pyridoxal50-phosphate(PLP), a PLP-dependent tyrosine decarboxylase(Os Ty DC1), and two duplicated hydroxycinnamoyl transferases(Os THT1 and Os THT2). These members were combined to represent an enzymological innovation gene cluster. Natural variation analysis showed that the abundance of the toxic tyramine intermediate of the gene cluster among different rice accessions is mainly determined by the coordinated transcription of Os Ty DC1 and Os THT1. Further pathogen incubation assays demonstrated that the end products of the HT gene cluster displayed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. Oryzae(Xoo) and fungal pathogen Magnaporthe oryzae(M. oryzae), and the enhanced resistance is associated with the boost of phytoalexins and the activation of defense response. The unique presence of the HT gene cluster in Oryza AA genome, together with the enrichment of transposon elements within this gene cluster region, provides an evolutionary background to accelerate cluster member combinations. Our study not only discovered a gene cluster involved in the phenylpropanoid metabolism but also addressed the key aspects of gene cluster formation. In addition, our results provide a new metabolic pool for plant defense against pathogens.展开更多
基金supported by grants from the Fundamental Research Funds for the Central Universities(KYCXJC2022003)the National Natural Science Foundation of China(32070243)+1 种基金the Outstanding Young Teacher of the QingLan Project of Jiangsu Province.Y.V.d.P.acknowledges funding from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01).
文摘MicroTom has a short growth cycle and high transformation efficiency,and is a prospective model plant for studying organ development,metabolism,and plant–microbe interactions.Here,with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments,we constructed multiple gene co-expression networks,which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth,e.g.arbuscular mycorrhizal symbiosis and fruit development.Additionally,non-coding RNAs,including miRNAs,lncRNAs,and circRNAs were also identified,together with their potential targets.Interacting networks between different types of non-coding RNAs(miRNA-lncRNA),and non-coding RNAs and genes(miRNA-mRNA and lncRNA-mRNA)were constructed as well.Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit.Lastly,we established a database(http://eplant.njau.edu.cn/microTomBase/)with genomic and transcriptomic data,as well as details of gene co-expression and interacting networks on MicroTom,and this database should be of great value to those who want to adopt MicroTom as a model plant for research.
基金supported by the National Science Fund for Distinguished Young Scholars of China (31625021)the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (31821005)+1 种基金the State Key Program of National Natural Science Foundation of China (31530052)the Hainan University Startup Fund (KYQD(ZR)1866)。
文摘Genomic clustering of non-homologous genes for the biosynthesis of plant defensive compounds is an emerging theme, but insights into their formation and physiological function remain limited. Here we report the identification of a newly discovered hydroxycinnamoyl tyramine(HT) gene cluster in rice.This cluster contains a pyridoxamine 50-phosphate oxidase(Os PDX3) producing the cofactor pyridoxal50-phosphate(PLP), a PLP-dependent tyrosine decarboxylase(Os Ty DC1), and two duplicated hydroxycinnamoyl transferases(Os THT1 and Os THT2). These members were combined to represent an enzymological innovation gene cluster. Natural variation analysis showed that the abundance of the toxic tyramine intermediate of the gene cluster among different rice accessions is mainly determined by the coordinated transcription of Os Ty DC1 and Os THT1. Further pathogen incubation assays demonstrated that the end products of the HT gene cluster displayed enhanced resistance to the bacterial pathogen Xanthomonas oryzae pv. Oryzae(Xoo) and fungal pathogen Magnaporthe oryzae(M. oryzae), and the enhanced resistance is associated with the boost of phytoalexins and the activation of defense response. The unique presence of the HT gene cluster in Oryza AA genome, together with the enrichment of transposon elements within this gene cluster region, provides an evolutionary background to accelerate cluster member combinations. Our study not only discovered a gene cluster involved in the phenylpropanoid metabolism but also addressed the key aspects of gene cluster formation. In addition, our results provide a new metabolic pool for plant defense against pathogens.
