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

SIMPLE SUMMARY: Mitragyna speciosa (Kratom) is a narcotic plant indigenous to Southeast Asian countries, including Thailand. Traditionally, M. speciosa has been used as medicine to treat diarrhea and has anti-coughing, analgesic, and fever-reducing properties. Its leaves are commonly chewed by workers during physical labor for their coca-like stimulant effect to increase stamina and endurance. To identify important bioactive alkaloids with potential pharmaceutical uses, we performed a whole genome sequencing of Kratom to obtain information relating to the gene content in its genome, which will facilitate an improved understanding of the biosynthesis pathway and provide resources for assessing the genetic diversity in M. speciosa. ABSTRACT: Mitragyna speciosa (Kratom) is a tropical narcotic plant native to Southeast Asia with unique pharmacological properties. Here, we report the first chromosome-scale assembly of the M. speciosa genome. We employed PacBio sequencing to obtain a preliminary assembly, which was subsequently scaffolded using the chromatin contact mapping technique (Hi-C) into 22 pseudomolecules. The final assembly was 692 Mb with a scaffold N50 of 26 Mb. We annotated a total of 39,708 protein-coding genes, and our gene predictions recovered 98.4% of the highly conserved orthologs based on the BUSCO analysis. The phylogenetic analysis revealed that M. speciosa diverged from the last common ancestors of Coffea arabica and Coffea canephora approximately 47.6 million years ago. Our analysis of the sequence divergence at fourfold-degenerate sites from orthologous gene pairs provided evidence supporting a genome-wide duplication in M. speciosa, agreeing with the report that members of the genus Mitragyna are tetraploid. The STRUCTURE and principal component analyses demonstrated that the 85 M. speciosa accessions included in this study were an admixture of two subpopulations. The availability of our high-quality chromosome-level genome assembly and the transcriptomic resources will be useful for future studies on the alkaloid biosynthesis pathway, as well as comparative phylogenetic studies in Mitragyna and related species.