The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

[1]  L. Caputi,et al.  Single-cell multi-omics in the medicinal plant Catharanthus roseus , 2023, Nature Chemical Biology.

[2]  Nanna Bjarnholt,et al.  Spatial localization of monoterpenoid indole alkaloids in Rauvolfia tetraphylla by high resolution mass spectrometry imaging. , 2023, Phytochemistry.

[3]  H. Jansen,et al.  An updated version of the Madagascar periwinkle genome , 2022, F1000Research.

[4]  Y. Li,et al.  Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism , 2022, Nature Plants.

[5]  Jeremy S. Morris,et al.  Alkaloid binding to opium poppy major latex proteins triggers structural modification and functional aggregation , 2022, Nature Communications.

[6]  H. Jansen,et al.  Genome Assembly of the Medicinal Plant Voacanga thouarsii , 2022, Genome biology and evolution.

[7]  R. Dirks,et al.  The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis , 2022, G3.

[8]  J. Keasling,et al.  A microbial supply chain for production of the anti-cancer drug vinblastine , 2022, Nature.

[9]  L. Caputi,et al.  Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism , 2022, bioRxiv.

[10]  L. Caputi,et al.  Biosynthesis of strychnine , 2022, Nature.

[11]  R. Ciccocioppo,et al.  Yohimbine as a pharmacological probe for alcohol research: a systematic review of rodent and human studies , 2022, Neuropsychopharmacology.

[12]  G. Mustafa,et al.  Molecular Mechanisms and Therapeutic Strategies for Levodopa-Induced Dyskinesia in Parkinson’s Disease: A Perspective Through Preclinical and Clinical Evidence , 2022, Frontiers in Pharmacology.

[13]  S. O’Connor,et al.  More than a Catharanthus plant: A multicellular and pluri-organelle alkaloid-producing factory. , 2022, Current opinion in plant biology.

[14]  Yi Tang,et al.  Engineered Production of Strictosidine and Analogues in Yeast. , 2022, ACS synthetic biology.

[15]  N. Papon,et al.  Chromosome-scale genomes throw light on plant drug biosynthesis. , 2022, Trends in pharmacological sciences.

[16]  Xiaodi Hu,et al.  Chromosome-level assembly of Neolamarckia cadamba genome provides insights into the evolution of cadambine biosynthesis. , 2021, The Plant journal : for cell and molecular biology.

[17]  N. Kulagina,et al.  Enhanced bioproduction of anticancer precursor vindoline by yeast cell factories , 2021, Microbial biotechnology.

[18]  C. Smolke,et al.  Engineering cellular metabolite transport for biosynthesis of computationally predicted tropane alkaloid derivatives in yeast , 2021, Proceedings of the National Academy of Sciences.

[19]  Jianquan Liu,et al.  A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis , 2021, Nature Communications.

[20]  Jiming Jiang,et al.  The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health , 2021, G3.

[21]  Tetsuya Mori,et al.  Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis , 2021, Nature Communications.

[22]  S. O’Connor,et al.  Alternative splicing creates a pseudo-strictosidine β-d-glucosidase modulating alkaloid synthesis in Catharanthus roseus. , 2020, Plant physiology.

[23]  Ben Fulton,et al.  CAFE 5 models variation in evolutionary rates among gene families , 2020, Bioinform..

[24]  S. Koren,et al.  Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies , 2020, Genome Biology.

[25]  S. O’Connor,et al.  Identifying Missing Biosynthesis Enzymes of Plant Natural Products. , 2020, Trends in pharmacological sciences.

[26]  S. Kelly,et al.  OrthoFinder: phylogenetic orthology inference for comparative genomics , 2019, Genome Biology.

[27]  Linda V. Bakker,et al.  An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps , 2019, bioRxiv.

[28]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[29]  Thomas Peterson,et al.  Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline , 2019, Genome Biology.

[30]  Gina M. Pham,et al.  Gene Discovery in Gelsemium Highlights Conserved Gene Clusters in Monoterpene Indole Alkaloid Biosynthesis , 2018, Chembiochem : a European journal of chemical biology.

[31]  O. Safonova,et al.  Completion of the canonical pathway for assembly of anticancer drugs vincristine/vinblastine in Catharanthus roseus , 2018, The Plant journal : for cell and molecular biology.

[32]  Shujun Ou,et al.  Assessing genome assembly quality using the LTR Assembly Index (LAI) , 2018, Nucleic acids research.

[33]  S. O’Connor,et al.  Cytochrome P450 and O-methyltransferase catalyze the final steps in the biosynthesis of the anti-addictive alkaloid ibogaine from Tabernanthe iboga , 2018, The Journal of Biological Chemistry.

[34]  S. Taheri,et al.  Contribution of transposable elements in the plant's genome. , 2018, Gene.

[35]  Vincent Courdavault,et al.  Missing enzymes in the biosynthesis of the anticancer drug vinblastine in Madagascar periwinkle , 2018, Science.

[36]  Christophe Klopp,et al.  D-GENIES: dot plot large genomes in an interactive, efficient and simple way , 2018, PeerJ.

[37]  B. Schneider,et al.  A BAHD acyltransferase catalyzing 19‐O‐acetylation of tabersonine derivatives in roots of Catharanthus roseus enables combinatorial synthesis of monoterpene indole alkaloids , 2018, The Plant journal : for cell and molecular biology.

[38]  S. O’Connor,et al.  Sarpagan bridge enzyme has substrate-controlled cyclization and aromatization modes , 2018, Nature Chemical Biology.

[39]  G. Glevarec,et al.  Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks , 2018, Scientific Reports.

[40]  L. Caputi,et al.  Discovery of a Short‐Chain Dehydrogenase from Catharanthus roseus that Produces a New Monoterpene Indole Alkaloid , 2018, Chembiochem : a European journal of chemical biology.

[41]  J. Hájíček,et al.  Solution of the multistep pathway for assembly of corynanthean, strychnos, iboga, and aspidosperma monoterpenoid indole alkaloids from 19E-geissoschizine , 2018, Proceedings of the National Academy of Sciences.

[42]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[43]  Yu Lin,et al.  Assembly of long, error-prone reads using repeat graphs , 2018, Nature Biotechnology.

[44]  C. Buell,et al.  Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides , 2017, G3: Genes, Genomes, Genetics.

[45]  S. O’Connor,et al.  A three enzyme system to generate the Strychnos alkaloid scaffold from a central biosynthetic intermediate , 2017, Nature Communications.

[46]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[47]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[48]  Olivier Langella,et al.  X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. , 2017, Journal of proteome research.

[49]  S. Maury,et al.  Folivory elicits a strong defense reaction in Catharanthus roseus: metabolomic and transcriptomic analyses reveal distinct local and systemic responses , 2017, Scientific Reports.

[50]  Timothy L. Tickle,et al.  A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. , 2017, Cell reports.

[51]  Tracey A Ruhlman,et al.  The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae , 2016, Scientific Reports.

[52]  L. Caputi,et al.  Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity , 2016, Nature Communications.

[53]  Felipe A. Simão BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs , 2016 .

[54]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[55]  Brijesh Kumar,et al.  Rapid fingerprinting of Rauwolfia species using direct analysis in real time mass spectrometry combined with principal component analysis for their discrimination , 2015 .

[56]  G. Glevarec,et al.  Phytochemical genomics of the Madagascar periwinkle: Unravelling the last twists of the alkaloid engine. , 2015, Phytochemistry.

[57]  F. Geu-Flores,et al.  Discovery of a P450-catalyzed step in vindoline biosynthesis: a link between the aspidosperma and eburnamine alkaloids. , 2015, Chemical communications.

[58]  L. Caputi,et al.  Unlocking the Diversity of Alkaloids in Catharanthus roseus: Nuclear Localization Suggests Metabolic Channeling in Secondary Metabolism , 2015, Chemistry & biology.

[59]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[60]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[61]  N. Papon,et al.  A look inside an alkaloid multisite plant: the Catharanthus logistics. , 2014, Current opinion in plant biology.

[62]  Brian Bushnell,et al.  BBMap: A Fast, Accurate, Splice-Aware Aligner , 2014 .

[63]  F. Geu-Flores,et al.  A Pair of Tabersonine 16-Hydroxylases Initiates the Synthesis of Vindoline in an Organ-Dependent Manner in Catharanthus roseus1[C][W] , 2013, Plant Physiology.

[64]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[65]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity , 2013 .

[66]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[67]  Shikha Gupta,et al.  Bioactivity guided isolation of antipsychotic constituents from the leaves of Rauwolfia tetraphylla L. , 2012, Fitoterapia.

[68]  Shikha Gupta,et al.  HPTLC method for the simultaneous determination of four indole alkaloids in Rauwolfia tetraphylla: a study of organic/green solvent and continuous/pulse sonication. , 2012, Journal of pharmaceutical and biomedical analysis.

[69]  Shikha Gupta,et al.  A SIMPLE ISOCRATIC HPLC METHOD FOR THE SIMULTANEOUS DETERMINATION OF ANTIPSYCHOTIC INDOLE ALKALOIDS IN RAUWOLFIA TETRAPHYLLA , 2012 .

[70]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[71]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[72]  B. Usadel,et al.  PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA] , 2011, Plant Cell.

[73]  V. Courdavault,et al.  Strictosidine activation in Apocynaceae: towards a "nuclear time bomb"? , 2010, BMC Plant Biology.

[74]  S. Delrot,et al.  Purification and functional characterization of protoplasts and intact vacuoles from grape cells , 2010, BMC Research Notes.

[75]  Michael S. Barker,et al.  EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics , 2010, Evolutionary bioinformatics online.

[76]  Thomas L. Madden,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[77]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[78]  Yu Zhao,et al.  Purification, cloning, functional expression and characterization of perakine reductase: the first example from the AKR enzyme family, extending the alkaloidal network of the plant Rauvolfia , 2008, Plant Molecular Biology.

[79]  L. Szabó Molecular evolutionary lines in the formation of indole alkaloids derived from secologanin , 2008 .

[80]  S. O’Connor,et al.  Chemistry and biology of monoterpene indole alkaloid biosynthesis. , 2006, Natural product reports.

[81]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[82]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[83]  Anders Gorm Pedersen,et al.  RevTrans: multiple alignment of coding DNA from aligned amino acid sequences , 2003, Nucleic Acids Res..

[84]  Xueyan Ma,et al.  Heterologous expression of a Rauvolfia cDNA encoding strictosidine glucosidase, a biosynthetic key to over 2000 monoterpenoid indole alkaloids. , 2002, European journal of biochemistry.

[85]  Bin Ma,et al.  PatternHunter: faster and more sensitive homology search , 2002, Bioinform..

[86]  J. Memelink,et al.  Geraniol 10‐hydroxylase1, a cytochrome P450 enzyme involved in terpenoid indole alkaloid biosynthesis , 2001, FEBS letters.

[87]  J. Memelink,et al.  Biotransformation of tryptamine and secologanin into plant terpenoid indole alkaloids by transgenic yeast , 2001, Applied Microbiology and Biotechnology.

[88]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[89]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[90]  S. Podos,et al.  The effect of corynanthine on intraocular pressure in clinical trials. , 1985, Ophthalmology.

[91]  B. Perry,et al.  [3H]rauwolscine (α-yohimbine): A specific antagonist radioligand for brain α2-adrenergic receptors , 1981 .

[92]  M. M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[93]  U. K. Laemmli,et al.  Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 , 1970, Nature.

[94]  V. Courdavault,et al.  Predicting Monoterpene Indole Alkaloid-Related Genes from Expression Data with Artificial Neural Networks. , 2022, Methods in molecular biology.

[95]  G. Glevarec,et al.  Deciphering the Evolution, Cell Biology and Regulation of Monoterpene Indole Alkaloids , 2013 .

[96]  H. Wickham ggplot2 , 2011 .

[97]  R. Schiestl,et al.  Large-scale high-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method , 2007, Nature Protocols.

[98]  J. Stöckigt Enzymatic formation of intermediates in the biosynthests of ajmalicine: Strictosidine and cathenamine , 1979 .

[99]  H. Husson,et al.  Isolation and biomimetic conversion of 4,21-dehydrogeissoschizine , 1979 .

[100]  S. K. Sleigh,et al.  ‘One-pot’ biomimetic synthesis of 19β-heteroyohimbine alkaloids , 1977 .

[101]  M. Zenk,et al.  Strictosidine (isovincoside): the key intermediate in the biosynthesis of monoterpenoid indole alkaloids , 1977 .

[102]  Jens Roat Kultima,et al.  Bioinformatics Applications Note Genome Analysis Genoplotr: Comparative Gene and Genome Visualization in R , 2022 .