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Iamsaard S, Arun S, Burawat J, Yannasithinon S, Tongpan S, Bunsueb S, Lapyuneyong N, Choowong-in P, Tangsrisakda N, Chaimontri C, Sukhorum W. Evaluation of antioxidant capacity and reproductive toxicity of aqueous extract of Thai Mucuna pruriens seeds. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2020; 18:265-273. [DOI: 10.1016/j.joim.2020.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/04/2020] [Indexed: 01/23/2023]
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Sathyanarayana N, Pittala RK, Tripathi PK, Chopra R, Singh HR, Belamkar V, Bhardwaj PK, Doyle JJ, Egan AN. Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. BMC Genomics 2017; 18:409. [PMID: 28545396 PMCID: PMC5445377 DOI: 10.1186/s12864-017-3780-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/10/2017] [Indexed: 12/14/2022] Open
Abstract
Background The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. Results One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. Conclusions The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3780-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- N Sathyanarayana
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India.
| | - Ranjith Kumar Pittala
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Pankaj Kumar Tripathi
- Department of Botany, Sikkim University, 6th Mile, Tadong-737102, Gangtok, Sikkim, India
| | - Ratan Chopra
- United States Department of Agriculture, Agriculture Research Service, 3810 4th St., Lubbock, TX, 79415, USA
| | - Heikham Russiachand Singh
- Department of Plant Science, McGill University, Raymond Building, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, H9X 3V9, Canada
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Pardeep Kumar Bhardwaj
- Institute of Bioresources and Sustainable Development, ikkim Centre, Tadong-737102, Gangtok, Sikkim, India
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 412 Mann Library, Ithaca, NY, 14853, USA
| | - Ashley N Egan
- Department of Botany, Smithsonian Institution, National Museum of Natural History, US National Herbarium, 10th and Constitution Ave NW, Washington, DC, 20013, USA.
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Ismail NZ, Arsad H, Samian MR, Ab Majid AH, Hamdan MR. Evaluation of genetic diversity of Clinacanthus nutans (Acanthaceaea) using RAPD, ISSR and RAMP markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:523-534. [PMID: 27924125 PMCID: PMC5120048 DOI: 10.1007/s12298-016-0391-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/17/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Three polymerase chain reaction (PCR) techniques were compared to analyse the genetic diversity of Clinacanthus nutans eight populations in the northern region of Peninsular Malaysia. The PCR techniques were random amplified polymorphic deoxyribonucleic acids (RAPD), inter-simple sequence repeats (ISSR) and random amplified microsatellite polymorphisms (RAMP). Leaf genomic DNA was PCR amplified using 17 RAPD, 8 ISSR and 136 RAMP primers . However, only 10 RAPD primers, 5 ISSR primers and 37 RAMP primers produced reproducible bands. The results were evaluated for polymorphic information content (PIC), marker index (MI) and resolving power (RP). The RAMP marker was the most useful marker compared to RAPD and ISSR markers because it showed the highest average value of PIC (0.25), MI (11.36) and RP (2.86). The genetic diversity showed a high percentage of polymorphism at the species level compared to the population level. Furthermore, analysis of molecular variance revealed that the genetic diversity was higher within populations, as compared to among populations of C. nutans. From the results, the RAMP technique was recommended for the analysis of genetic diversity of C. nutans.
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Affiliation(s)
- Noor Zafirah Ismail
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
| | - Hasni Arsad
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
| | - Mohammed Razip Samian
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang Malaysia
| | - Abdul Hafiz Ab Majid
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang Malaysia
| | - Mohammad Razak Hamdan
- Central Drug Research Institute, Universiti Sains Malaysia, 11800 Gelugor, Penang Malaysia
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