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

View ORCID ProfileKyo Bin Kang, View ORCID ProfileMadeleine Ernst, View ORCID ProfileJustin J. J. van der Hooft, Ricardo R. da Silva, Junha Park, View ORCID ProfileMarnix H. Medema, View ORCID ProfileSang Hyun Sung, View ORCID ProfilePieter C. Dorrestein
doi: https://doi.org/10.1101/463620
Kyo Bin Kang
1Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
2College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Republic of Korea
3College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
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  • For correspondence: kbkang@sookmyung.ac.kr pdorrestein@ucsd.edu
Madeleine Ernst
1Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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Justin J. J. van der Hooft
1Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
4Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
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Ricardo R. da Silva
1Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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Junha Park
3College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Marnix H. Medema
4Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands
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Sang Hyun Sung
3College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Pieter C. Dorrestein
1Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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  • For correspondence: kbkang@sookmyung.ac.kr pdorrestein@ucsd.edu
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SUMMARY

Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped specialized metabolite diversity, which drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating specialized metabolite diversity in an evolutionary context have been limited by the impossibility to identify 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 for 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 the dark plant metabolomics matter. To gain insights in substructural diversity within the 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 predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations towards the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms.

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  • ↵b Deceased July 24, 2018.

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Posted November 07, 2018.
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Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
Kyo Bin Kang, Madeleine Ernst, Justin J. J. van der Hooft, Ricardo R. da Silva, Junha Park, Marnix H. Medema, Sang Hyun Sung, Pieter C. Dorrestein
bioRxiv 463620; doi: https://doi.org/10.1101/463620
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Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
Kyo Bin Kang, Madeleine Ernst, Justin J. J. van der Hooft, Ricardo R. da Silva, Junha Park, Marnix H. Medema, Sang Hyun Sung, Pieter C. Dorrestein
bioRxiv 463620; doi: https://doi.org/10.1101/463620

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