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A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
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Document Title
A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
Author
Pootakham W, Yoocha T, Jomchai N, Kongkachana W, Naktang C, Sonthirod C, Chowpongpang S, Aumpuchin P, Tangphatsornruang S
Name from Authors Collection
Scopus Author ID
57201312649
Scopus Author ID
36059124300
Scopus Author ID
56030033100
Affiliations
National Science & Technology Development Agency - Thailand; National Science & Technology Development Agency - Thailand
Type
Article
Source Title
BIOLOGY-BASEL
Year
2022
Volume
11
Issue
12
Open Access
gold, Green Published
Publisher
MDPI
DOI
10.3390/biology11101492
Format
Abstract
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. 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.
Keyword
Chromosome-scale genome assembly | Genetic diversity | Hi-C | Iso-seq | Mitragyna | PacBio
Funding Sponsor
National Science and Technology Development Agency, Thailand [P2051919, 1000221]
License
CC BY
Rights
Authors
Publication Source
WOS