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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 worke...

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Autores principales: Pootakham, Wirulda, Yoocha, Thippawan, Jomchai, Nukoon, Kongkachana, Wasitthee, Naktang, Chaiwat, Sonthirod, Chutima, Chowpongpang, Srimek, Aumpuchin, Panyavut, Tangphatsornruang, Sithichoke
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9598492/
https://www.ncbi.nlm.nih.gov/pubmed/36290398
http://dx.doi.org/10.3390/biology11101492
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author Pootakham, Wirulda
Yoocha, Thippawan
Jomchai, Nukoon
Kongkachana, Wasitthee
Naktang, Chaiwat
Sonthirod, Chutima
Chowpongpang, Srimek
Aumpuchin, Panyavut
Tangphatsornruang, Sithichoke
author_facet Pootakham, Wirulda
Yoocha, Thippawan
Jomchai, Nukoon
Kongkachana, Wasitthee
Naktang, Chaiwat
Sonthirod, Chutima
Chowpongpang, Srimek
Aumpuchin, Panyavut
Tangphatsornruang, Sithichoke
author_sort Pootakham, Wirulda
collection PubMed
description 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.
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spelling pubmed-95984922022-10-27 A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand Pootakham, Wirulda Yoocha, Thippawan Jomchai, Nukoon Kongkachana, Wasitthee Naktang, Chaiwat Sonthirod, Chutima Chowpongpang, Srimek Aumpuchin, Panyavut Tangphatsornruang, Sithichoke Biology (Basel) Article 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. MDPI 2022-10-12 /pmc/articles/PMC9598492/ /pubmed/36290398 http://dx.doi.org/10.3390/biology11101492 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Pootakham, Wirulda
Yoocha, Thippawan
Jomchai, Nukoon
Kongkachana, Wasitthee
Naktang, Chaiwat
Sonthirod, Chutima
Chowpongpang, Srimek
Aumpuchin, Panyavut
Tangphatsornruang, Sithichoke
A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
title A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
title_full A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
title_fullStr A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
title_full_unstemmed A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
title_short A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand
title_sort chromosome-scale genome assembly of mitragyna speciosa (kratom) and the assessment of its genetic diversity in thailand
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9598492/
https://www.ncbi.nlm.nih.gov/pubmed/36290398
http://dx.doi.org/10.3390/biology11101492
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