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

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 production of bioactive alkaloids in heterologous hosts.

A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand

“…Here, we present a de novo assembly of the M. speciosa genome using the combination of PacBio long-read SMRT technology and the long-range proximity ligation technique (Hi-C). The preliminary assembly obtained from the PacBio sequencing was 692 Mb, slightly smaller than our estimated genome size of 727 Mb (by DNA flow cytometry) and a previously reported genome size of 780 Mb [ 6 ]. We subsequently employed the Hi-C method to identify chromosomal interactions using chromosome conformation capture.…”

“…This draft assembly was subsequently scaffolded using the long-range chromatin fixation technique (Hi-C) into a chromosome-level assembly containing 22 pseudomolecules > 10 Mb in length (from here on, they will be referred to as chromosomes; Figure 2 , Supplementary Figure S3 ). The genus Mitragyna has been reported as a tetraploid with a base chromosome number of 11 (2 n = 4 x = 44) [ 5 , 6 ]. The 22 chromosomes corresponded to the diploid chromosome number and covered 602 Mb, or 87.04% of the 692-Mb assembly.…”

“…Kiehn (1995) reported that Mitragyna species are tetraploid with a chromosome number of 2 n = 4 x = 44 [ 5 ]. Chromosome staining with DAPI was also carried out to confirm the chromosome number of 44 in the mitotic metaphase [ 6 ]. However, the identity of progenitor species that underwent hybridization to give rise to M. speciosa is currently unknown.…”

“…In addition to mitragynine, 54 known alkaloids have successfully been isolated and identified in this species. Due to interest in a diverse range of bioactive alkaloids produced by M. speciosa , the draft genome sequence has recently been assembled using the linked-read 10× Genomics technology [ 6 ]. The reported assembly encompasses 1.12 Gb and contains 17,031 scaffolds with an N50 scaffold size of 1.02 Mb.…”

Utilizing Plant Synthetic Biology to Improve Human Health and Wellness

“…Historically, medicinal plant extracts have been used as food additives, but introduction of their biosynthetic pathways into common food crops offers a means of increasing the availability of nutraceuticals to a broader market. In some cases, the biosynthetic pathways are known (see Yang et al, 2016 for an in-depth review) and efforts are being made to sequence more medicinal plant genomes in order to accelerate enzyme discovery in candidate organisms ( Brose et al, 2021 ). Nevertheless, the major limiting step hampering efforts to engineer plant nutraceuticals is still the discovery of the enzymes involved in the biosynthesis of target plant natural products.…”