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. 2021 Apr 15;11(4):jkab058.
doi: 10.1093/g3journal/jkab058.

The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health

Julia Brose  1 , Kin H Lau  1 , Thu Thuy Thi Dang  2 , John P Hamilton  1 , Lívia do Vale Martins  1   3 , Britta Hamberger  4 , Bjoern Hamberger  4 , Jiming Jiang  1   5   6 , Sarah E O'Connor  7 , C Robin Buell  1   6   8
Affiliations

The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health

Julia Brose et al. G3 (Bethesda). .

Abstract

Mitragyna speciosa (kratom) produces numerous compounds with pharmaceutical properties including the production of bioactive monoterpene indole and oxindole alkaloids. Using a linked-read approach, a 1,122,519,462 bp draft assembly of M. speciosa "Rifat" was generated with an N50 scaffold size of 1,020,971 bp and an N50 contig size of 70,448 bp that encodes 55,746 genes. Chromosome counting revealed that "Rifat" is a tetraploid with a base chromosome number of 11, which was further corroborated by orthology and syntenic analysis of the genome. Analysis of genes and clusters involved in specialized metabolism revealed genes putatively involved in alkaloid biosynthesis. Access to the genome of M. speciosa will facilitate an improved understanding of alkaloid biosynthesis and accelerate the production of bioactive alkaloids in heterologous hosts.

Keywords: Mitragyna speciosa; alkaloids; genome; kratom; linked-read assembly.

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Figures

Figure 1
Figure 1
Structural diversity of alkaloids from M. speciosa. Red structures signify compounds with reported pharmaceutical properties. Photo credit: Jade at the Healing East.
Figure 2
Figure 2
Mitotic metaphase chromosomes of M. speciosa. Digested meristems from root tips counterstained with DAPI pictured in blue. Bar = 5 μm.
Figure 3
Figure 3
Phylogeny of M. speciosa and other angiosperms. Phylogeny was obtained from Orthofinder (v2.2.7; Emms and Kelly 2019). Photo credit: Sangtea Kim (Amborella trichopoda picture).
Figure 4
Figure 4
Orthogroups of M. speciosa from Orthofinder (v2.2.7; Emms and Kelly 2019). The number of orthogroups identified between Amborella trichopoda, Arabidopsis thaliana, Vitis vinifera, Solanum lycopersicum, Theobroma cacao, Coffea canephora, and M. speciosa. The numbers on top of each bar are the number of orthogroups that are present amount the species with black-filled circles below the x-axis. The proportion of the species present in orthogroups is shown to the left of the axis.
Figure 5
Figure 5
Frequency of orthogroups with various numbers of M. speciosa genes per one gene of other species. Amborella trichopoda, Arabidopsis thaliana, Vitis vinifera, Solanum lycopersicum, Theobroma cacao, and Coffea canephora are the species were only one gene is present in the orthogroups. Frequency refers to the number of orthogroups identified by Orthofinder (v2.2.7; Emms and Kelly 2019). Orthogroups are separated by the number of M. speciosa genes present when the orthogroup contains one gene from A. trichopoda, A. thaliana, V. vinifera, S. lycopersicum, T. cacao, and C. canephora.
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