Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

The Plant Journal : for Cell and Molecular Biology
Kyo Bin KangPieter C Dorrestein


Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped the diversity of specialized metabolites, which then drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating the diversity of specialized metabolites in an evolutionary context have been limited by the impossibility of identifying chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites and apply it to over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5% based on spectral library matches alone to 42.6% of total MS/MS molecular features, extending annotations from well-known plant compound classes into dark plant metabolomics. To gain insights into substructural diversity within this plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predo...Continue Reading


Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Sep 19, 2000·American Journal of Botany·J E RichardsonM W Chase
Nov 3, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·J E RichardsonM D Pirie
Aug 12, 2008·Drug Discovery Today·Alan L Harvey
May 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jeramie WatrousPieter C Dorrestein
Mar 28, 2013·Analytical and Bioanalytical Chemistry·Ryo Nakabayashi, Kazuki Saito
Jun 27, 2013·Proceedings of the National Academy of Sciences of the United States of America·Don Duy NguyenPieter C Dorrestein
Sep 1, 2007·Metabolomics : Official Journal of the Metabolomic Society·Lloyd W SumnerMark R Viant
Mar 29, 2014·Natural Product Reports·Madeleine ErnstNorberto Peporine Lopes
Oct 11, 2014·Nucleic Acids Research·Priyanka BanerjeeMathias Dunkel
Oct 29, 2014·Nature Communications·Meng-Jun LiuLong-Hai Luo
Jan 23, 2015·Evolution; International Journal of Organic Evolution·Renske E OnsteinH Peter Linder
Sep 24, 2015·Proceedings of the National Academy of Sciences of the United States of America·Kai DührkopSebastian Böcker
Oct 3, 2015·Proceedings of the National Academy of Sciences of the United States of America·Ricardo R da SilvaRobert A Quinn
Feb 3, 2016·Journal of Cheminformatics·Christoph RuttkiesSteffen Neumann
Feb 18, 2016·Analytical Chemistry·Pierre-Marie AllardJean-Luc Wolfender
Aug 31, 2016·Nature Communications·Nir ShahafAsaph Aharoni
Sep 13, 2016·Journal of Natural Products·Kyo Bin KangSang Hyun Sung
Sep 18, 2016·Proceedings of the National Academy of Sciences of the United States of America·Ruiqi HuangTodd J Barkman
Nov 20, 2016·Proceedings of the National Academy of Sciences of the United States of America·Justin J J van der HooftSimon Rogers
Nov 22, 2016·Journal of Cheminformatics·Yannick Djoumbou FeunangDavid S Wishart
Nov 16, 2017·Nucleic Acids Research·Dennis A BensonEric W Sayers
Apr 19, 2018·PLoS Computational Biology·Ricardo R da SilvaPieter C Dorrestein


Jan 11, 2020·The Plant Journal : for Cell and Molecular Biology·Paul D FraserAlisdair R Fernie
Dec 12, 2019·Natural Product Reports·Marc G ChevretteFrancisco Barona-Gómez
Jul 19, 2019·Metabolites·Madeleine ErnstJustin J J van der Hooft
Nov 12, 2019·Frontiers in Plant Science·Adriano RutzPierre-Marie Allard
Jun 11, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Kwangho SongIn Jin Ha
Mar 7, 2021·Metabolites·Karen McLuskeyRónán Daly

Related Concepts

Immunoglobulin Isotypes
Microscopy, Fluorescence
Protein O-Methyltransferase
Mass Spectrometry
Anatomical Space Structure
Leptopsylla segnis

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Pediculosis pubis

Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.

Rh Isoimmunization

Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.

Enzyme Evolution

This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Pharmacology of Proteinopathies

This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.