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Genome‐guided investigation of plant natural product biosynthesis
Author(s) -
Kellner Franziska,
Kim Jeongwoon,
Clavijo Bernardo J.,
Hamilton John P.,
Childs Kevin L.,
Vaillancourt Brieanne,
Cepela Jason,
Habermann Marc,
Steuernagel Burkhard,
Clissold Leah,
McLay Kirsten,
Buell Carol Robin,
O'Connor Sarah E.
Publication year - 2015
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12827
Subject(s) - genome , biology , gene , biosynthesis , computational biology , gene duplication , genetics
Summary The medicinal plant Madagascar periwinkle, C atharanthus roseus (L.) G. Don, produces hundreds of biologically active monoterpene‐derived indole alkaloid ( MIA ) metabolites and is the sole source of the potent, expensive anti‐cancer compounds vinblastine and vincristine. Access to a genome sequence would enable insights into the biochemistry, control, and evolution of genes responsible for MIA biosynthesis. However, generation of a near‐complete, scaffolded genome is prohibitive to small research communities due to the expense, time, and expertise required. In this study, we generated a genome assembly for C. roseus that provides a near‐comprehensive representation of the genic space that revealed the genomic context of key points within the MIA biosynthetic pathway including physically clustered genes, tandem gene duplication, expression sub‐functionalization, and putative neo‐functionalization. The genome sequence also facilitated high resolution co‐expression analyses that revealed three distinct clusters of co‐expression within the components of the MIA pathway. Coordinated biosynthesis of precursors and intermediates throughout the pathway appear to be a feature of vinblastine/vincristine biosynthesis. The C. roseus genome also revealed localization of enzyme‐rich genic regions and transporters near known biosynthetic enzymes, highlighting how even a draft genome sequence can empower the study of high‐value specialized metabolites.