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Research Article

volume 54 issue 5 (october 2020) : 635-640,   Doi: 10.18805/IJARe.A-508

Clarification of Sumatran Mulberry (Morus macroura var. macroura, Moraceae) from West Sumatra, Indonesia using Nucleus Ribosomal ITS (Internal Transcribed Spacer) Gene

E
Erma Nuratika
N
Nindi Aseny
S
Syamsuardi
N
Nurainas
F
Fitmawati
F
Friardi
1Department of Biology, Faculty of Mathematics and Natural Sciences, Andalas University, Padang 25163, Indonesia. 
Cite article:- Nuratika Erma, Aseny Nindi, Syamsuardi, Nurainas, Fitmawati, Friardi (2020). Clarification of Sumatran Mulberry (Morus macroura var. macroura, Moraceae) from West Sumatra, Indonesia using Nucleus Ribosomal ITS (Internal Transcribed Spacer) Gene. Indian Journal of Agricultural Research. 54(5): 635-640. doi: 10.18805/IJARe.A-508.

ABSTRACT

Background: Morus macroura Miq. is a potential tree species belonging to the Mulberry group, and consider as flora identity of West Sumatra Province with local name is Andalas. This germplasm tropical tree species utilize widely by local West Sumatran people for various purposes such as wood material to construct the traditional house of ethnic Minangkabau and medicinal substance for multiple diseases. However, the population numbers of this species were decreased and rare due to overexploitation without effort for planting. Based on this reason, it is imperative to conserve and utilize sustainable Mulberry. There is a highlight confusion to clarify that M. macroura from Sumatra population similar to Himalayan Mulberry. For this reason, it is essential to define the crucial local M. macroura from Sumatra (Sumatran Mulberry) for its conservation and sustainable utilization.  
Methods: In this study, the leaves from seven individuals of M. macroura collected from West Sumatra were used for DNA extraction and processed to the next step of the analysis. Four individuals of Himalayan Mulberry and both of two out-group, White Mulberry (M. alba), and Black Mulberry (M. nigra) were used in this study. Polymerase chain reaction (PCR) amplification was performed using two ITS markers (ITS5-F and ITS4-R) with an annealing temperature of 55oC. The PCR products were purified and sequenced by Macrogen USA DNA Sequencing. The phyllogenetic relationship between seven accessions and two of out-group (M. alba and M. nigra) were analyzed using the MEGA6 program.  
Result: The result indicated that all of the accessions M. macroura from Sumatra were grouped into the same cluster and separated to the Himalayan Mulberry group. The differentiation between Sumatran Mulberry and other Mulberry reflected in morphological and haplotype differentiation indicated that the Sumatran Mulberry as the different group and suggested as a variety with scientific name is M. macroura Miq. var. macroura. This clarification is useful for conservation and sustainable utilization of this variety, a specific Mulberry from Sumatra.

REFERENCES

  1. Arbain, D. (2012). Inventory, Constituents and Conservation of Biologically Important Sumatran Plants. Natural Product Communication (NPC). 7: 799-806.
  2. Burland, T.G. (2000). DNASTAR’s Lasergence Sequence Analysis Software. Methods Molecular. Biology. 132: 71-91. 
  3. Casacci, L.P., Barbero, F. and Balletto, E. (2014). Evolutionarily significant unit concept and its applicability in biological conservation. Italian Journal of Zoology. 81: 182-193.
  4. Chen, S, Yao, H., Han, J., Liu, C., Song, J. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLOS ONE. 5: 1-8.
  5. Doh, E.J., Kim, J.H., Oh, S.E. and Lee. G. (2017). Identification and monitoring of Korean medicines derived from Cinnamomum spp. by using ITS and DNA marker. Genes Genom. 39: 101–109.
  6. Doyle, J.J. and Doyle, J.L. (1987). Rapid DNA isolation procedure from small quantities of fresh leaf tissue. Phytochemistry Bulletin. 19: 11–15.
  7. Farrag, E.K., Kassem, M.E.S., Bayoumi, D., Shaker, S.E., Afifi, M.S. (2017). The phytochemical study, phenolic profile and anti gastric ulcer activity of Morus macroura Miq. Fruits extract. Journal of Applied Pharmaceutical Science. 7: 152-160. 
  8. GBIF: The Global Biodiversity Information Facility (2019). What is GBIF? Available from https: //www.gbif.org/what-is-gbif [ Accessed 17 November 2019].
  9. Hall, T.A. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acid Symposium Series. 41: 95-98.
  10. Hao, D.C., Chen, S.L., Xiao, P.G. and Peng, Y. (2010). Authentication of medicinal plants by DNA-based markers and genomics. Chinese Herbal Medicines. 2: 250-261.
  11. Huda, M., Syamsuardi, Nurainas, Murni, P. and Maulidah, R. (2019). Genetic divergence landrace of langsat (Lansium parasiticum) from Siberut Island based on ITS and MatK markers. Indian Journal of Agricultural Research. 53: 338-342 
  12. Jawati, S. (2006). Study on morphological variation of Andalas tree (Morus macroura Miq.) in West Sumatra. Scientific Report for the Undergraduate Degree. Dept. Biology, Fac. of Math. and Nat. Sci. Andalas University, Padang. (in Indonesian). 
  13. Kim, W.J., Moon, B.C., Yang, S., Han, K.S., Choi, G. and Lee, A.Y. (2016). Rapid authentication of the herbal medicine plant species Aralia continentalis Kitag. and Angelica biserrata C.Q. Yuan and R.H. Shan using ITS2 Sequences and Multiplex-SCAR markers. Molecules. 21: 1-12.
  14. Mace, G.M. (2004). The role of taxonomy in species conservation. Philosophical Transaction of the Royal Society of London, B, 359: 711–719.
  15. Miquel, F.A.W. (1862). Sumatra III Zizne Plantenwereld. Amsterdam. 414.
  16. Muellner, A.N., Samuel, R., Johnson, S.A., Cheek, M., Pennington, T.D., Chase, M.W. (2003). Molecular Phylogenetics of Meliaceae (Sapindales) Based on Nuclear and Plastid DNA Sequences. American Journal of Botany. 90: 471-480.
  17. Moawed, M.M. (2015). Evaluation of morphological and anatomical characters for discrimination and verification of some Medicago sativa (L.) Cultivars. Indian Journal of Agricultural Research. 50:183-192
  18. NCBI. 2019. Http://www.ncbi.nlm.nhi.gov/ (Accessed, Nov 2019).
  19. Nei, M. and Tajima, F. (1981). DNA polymorphism detectable by restriction endonucleases. Genetics, 97: 145.
  20. Nepal, M.P. (2008). Systematics and Reproductive Biology of The Genus Morus L. (Moraceae). An Abstract of a Dissertation. Division of Biology, College of Art and Sciences. Kansas State University, Kansas.
  21. Rao, A.A., Chauhan, S.S. and Radhakharishnan R. (2011). Distribution, Variation and Conservation of Mulberry (Morus spp.) Genetic Resources in the Arid Zone of Rajasthan, India. Bioremediation, Biodiversity and Bioavailability © Global Science Book.
  22. Rao, R.V. and Hodgkin, T. (2002). Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue and Organ Culture. 68: 1-19
  23. Rozas, J., Sanches Del Barrio J.C., Messeguer, Rozas, X.R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19: 2496-2497.
  24. Saddhe, A.A. and Kumar, K. (2018). DNA Barcoding of Plants: Selection of Core Markers for Taxonomic Groups. Plant Science. Today. 5: 9-13. 
  25. Song, W.H., Wang, J. Bucheli, P., Zhang, P.F., Wei, D.Z. and Lu, Y.H. (2019). Phytochemical Profiles of Different Mulberry (Morus sp.) Species from China. Journal of Agriculture Food Chemistry. 7: 9133-9140
  26. Strbanovic, R. Simic, A. Postic, D. Zivanovic, T. Vuckovic, S. Pfaf-Dolovac, E. and Stanisav-ljevicalsimic, R. (2015). Yield and morphological traits in alfalfa varieties of different origin. Legume Research-An International Journal. 38: 434-441.
  27. Syamsuardi. (2015). Morphological and Genetic Diversity of Andalas Tree (Morus macroura Miq.) Flora Identity of West Sumatra and Their Sustainable Utilization. Promoting Conservation of Selected High-Value Indigenous Species of Sumatra. ITTO and BPTSTH. 42-53. Available online at www.balithut-kuok.org. (In Indonesian). 
  28. Techen, N., Parveen, I., Pan, Z. and Khan, IA. (2014). DNA barcoding of medicinal plant material for identification. Current Opinion Biotechnology. 25: 103-10. 
  29. The Plant List. 2013. http://www.theplantlist.org./ (Accessed November 16, 2019). 
  30. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997). The clustal-X Windows Interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 25: 4876-4882.
  31. Tripathy, S.K., Nayak, P.K. Lenka, D. Swain, D. Baisakh, B. Mohanty, P. Senapati, N. et al. (2016). Morphological diversity of local landraces and wild forms of mungbean. Legume Research-An International Journal. 39: 485-493.
  32. Turland, N.J., Wiersema, J.H., Barrie, F.R., Greuter, W., Hawksworth, D.L., Herendeen, P.S., et al. (2018). International Code of Nomenclature for algae, fungi and plants (Shenzhen Code). Adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books. (Accessed November 16, 2019).
  33. Yusfita, E. (2008). Ethnobotanical Study on Andalas Tree (Morus macroura Miq.). Master Thesis in Dept. Biology, Graduate Faculty andalas University, Padang (In Indonesian). 
  34. Zhang, Y.B. Yuan, Y. Pang, Y.X., Yu, F.L., Yuan, C., Wang, D. Hu, X. (2019). Phylogenetic Reconstruction and Divergence Time Estimation of Blumea DC. (Asteraceae: Inuleae) in China Based on nrDNA ITS and cpDNA trnL-F Sequences. Plants. 8: 1-19.
  35. Zhou, J. Wang, W. Liu, M. and Liu, Z. (2014). Molecular authentication of the traditional medicinal plant Peucedanum praeruptorum and its substitutes and adulterants by DNA-barcoding technique. Pharmacognosy Magazine. 10: 385-390.
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Indian Journal of Agricultural Research
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    Research Article

    volume 54 issue 5 (october 2020) : 635-640,   Doi: 10.18805/IJARe.A-508

    Clarification of Sumatran Mulberry (Morus macroura var. macroura, Moraceae) from West Sumatra, Indonesia using Nucleus Ribosomal ITS (Internal Transcribed Spacer) Gene

    E
    Erma Nuratika
    N
    Nindi Aseny
    S
    Syamsuardi
    N
    Nurainas
    F
    Fitmawati
    F
    Friardi
    1Department of Biology, Faculty of Mathematics and Natural Sciences, Andalas University, Padang 25163, Indonesia. 
    Cite article:- Nuratika Erma, Aseny Nindi, Syamsuardi, Nurainas, Fitmawati, Friardi (2020). Clarification of Sumatran Mulberry (Morus macroura var. macroura, Moraceae) from West Sumatra, Indonesia using Nucleus Ribosomal ITS (Internal Transcribed Spacer) Gene. Indian Journal of Agricultural Research. 54(5): 635-640. doi: 10.18805/IJARe.A-508.

    ABSTRACT

    Background: Morus macroura Miq. is a potential tree species belonging to the Mulberry group, and consider as flora identity of West Sumatra Province with local name is Andalas. This germplasm tropical tree species utilize widely by local West Sumatran people for various purposes such as wood material to construct the traditional house of ethnic Minangkabau and medicinal substance for multiple diseases. However, the population numbers of this species were decreased and rare due to overexploitation without effort for planting. Based on this reason, it is imperative to conserve and utilize sustainable Mulberry. There is a highlight confusion to clarify that M. macroura from Sumatra population similar to Himalayan Mulberry. For this reason, it is essential to define the crucial local M. macroura from Sumatra (Sumatran Mulberry) for its conservation and sustainable utilization.  
    Methods: In this study, the leaves from seven individuals of M. macroura collected from West Sumatra were used for DNA extraction and processed to the next step of the analysis. Four individuals of Himalayan Mulberry and both of two out-group, White Mulberry (M. alba), and Black Mulberry (M. nigra) were used in this study. Polymerase chain reaction (PCR) amplification was performed using two ITS markers (ITS5-F and ITS4-R) with an annealing temperature of 55oC. The PCR products were purified and sequenced by Macrogen USA DNA Sequencing. The phyllogenetic relationship between seven accessions and two of out-group (M. alba and M. nigra) were analyzed using the MEGA6 program.  
    Result: The result indicated that all of the accessions M. macroura from Sumatra were grouped into the same cluster and separated to the Himalayan Mulberry group. The differentiation between Sumatran Mulberry and other Mulberry reflected in morphological and haplotype differentiation indicated that the Sumatran Mulberry as the different group and suggested as a variety with scientific name is M. macroura Miq. var. macroura. This clarification is useful for conservation and sustainable utilization of this variety, a specific Mulberry from Sumatra.

    REFERENCES

    1. Arbain, D. (2012). Inventory, Constituents and Conservation of Biologically Important Sumatran Plants. Natural Product Communication (NPC). 7: 799-806.
    2. Burland, T.G. (2000). DNASTAR’s Lasergence Sequence Analysis Software. Methods Molecular. Biology. 132: 71-91. 
    3. Casacci, L.P., Barbero, F. and Balletto, E. (2014). Evolutionarily significant unit concept and its applicability in biological conservation. Italian Journal of Zoology. 81: 182-193.
    4. Chen, S, Yao, H., Han, J., Liu, C., Song, J. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLOS ONE. 5: 1-8.
    5. Doh, E.J., Kim, J.H., Oh, S.E. and Lee. G. (2017). Identification and monitoring of Korean medicines derived from Cinnamomum spp. by using ITS and DNA marker. Genes Genom. 39: 101–109.
    6. Doyle, J.J. and Doyle, J.L. (1987). Rapid DNA isolation procedure from small quantities of fresh leaf tissue. Phytochemistry Bulletin. 19: 11–15.
    7. Farrag, E.K., Kassem, M.E.S., Bayoumi, D., Shaker, S.E., Afifi, M.S. (2017). The phytochemical study, phenolic profile and anti gastric ulcer activity of Morus macroura Miq. Fruits extract. Journal of Applied Pharmaceutical Science. 7: 152-160. 
    8. GBIF: The Global Biodiversity Information Facility (2019). What is GBIF? Available from https: //www.gbif.org/what-is-gbif [ Accessed 17 November 2019].
    9. Hall, T.A. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acid Symposium Series. 41: 95-98.
    10. Hao, D.C., Chen, S.L., Xiao, P.G. and Peng, Y. (2010). Authentication of medicinal plants by DNA-based markers and genomics. Chinese Herbal Medicines. 2: 250-261.
    11. Huda, M., Syamsuardi, Nurainas, Murni, P. and Maulidah, R. (2019). Genetic divergence landrace of langsat (Lansium parasiticum) from Siberut Island based on ITS and MatK markers. Indian Journal of Agricultural Research. 53: 338-342 
    12. Jawati, S. (2006). Study on morphological variation of Andalas tree (Morus macroura Miq.) in West Sumatra. Scientific Report for the Undergraduate Degree. Dept. Biology, Fac. of Math. and Nat. Sci. Andalas University, Padang. (in Indonesian). 
    13. Kim, W.J., Moon, B.C., Yang, S., Han, K.S., Choi, G. and Lee, A.Y. (2016). Rapid authentication of the herbal medicine plant species Aralia continentalis Kitag. and Angelica biserrata C.Q. Yuan and R.H. Shan using ITS2 Sequences and Multiplex-SCAR markers. Molecules. 21: 1-12.
    14. Mace, G.M. (2004). The role of taxonomy in species conservation. Philosophical Transaction of the Royal Society of London, B, 359: 711–719.
    15. Miquel, F.A.W. (1862). Sumatra III Zizne Plantenwereld. Amsterdam. 414.
    16. Muellner, A.N., Samuel, R., Johnson, S.A., Cheek, M., Pennington, T.D., Chase, M.W. (2003). Molecular Phylogenetics of Meliaceae (Sapindales) Based on Nuclear and Plastid DNA Sequences. American Journal of Botany. 90: 471-480.
    17. Moawed, M.M. (2015). Evaluation of morphological and anatomical characters for discrimination and verification of some Medicago sativa (L.) Cultivars. Indian Journal of Agricultural Research. 50:183-192
    18. NCBI. 2019. Http://www.ncbi.nlm.nhi.gov/ (Accessed, Nov 2019).
    19. Nei, M. and Tajima, F. (1981). DNA polymorphism detectable by restriction endonucleases. Genetics, 97: 145.
    20. Nepal, M.P. (2008). Systematics and Reproductive Biology of The Genus Morus L. (Moraceae). An Abstract of a Dissertation. Division of Biology, College of Art and Sciences. Kansas State University, Kansas.
    21. Rao, A.A., Chauhan, S.S. and Radhakharishnan R. (2011). Distribution, Variation and Conservation of Mulberry (Morus spp.) Genetic Resources in the Arid Zone of Rajasthan, India. Bioremediation, Biodiversity and Bioavailability © Global Science Book.
    22. Rao, R.V. and Hodgkin, T. (2002). Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue and Organ Culture. 68: 1-19
    23. Rozas, J., Sanches Del Barrio J.C., Messeguer, Rozas, X.R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19: 2496-2497.
    24. Saddhe, A.A. and Kumar, K. (2018). DNA Barcoding of Plants: Selection of Core Markers for Taxonomic Groups. Plant Science. Today. 5: 9-13. 
    25. Song, W.H., Wang, J. Bucheli, P., Zhang, P.F., Wei, D.Z. and Lu, Y.H. (2019). Phytochemical Profiles of Different Mulberry (Morus sp.) Species from China. Journal of Agriculture Food Chemistry. 7: 9133-9140
    26. Strbanovic, R. Simic, A. Postic, D. Zivanovic, T. Vuckovic, S. Pfaf-Dolovac, E. and Stanisav-ljevicalsimic, R. (2015). Yield and morphological traits in alfalfa varieties of different origin. Legume Research-An International Journal. 38: 434-441.
    27. Syamsuardi. (2015). Morphological and Genetic Diversity of Andalas Tree (Morus macroura Miq.) Flora Identity of West Sumatra and Their Sustainable Utilization. Promoting Conservation of Selected High-Value Indigenous Species of Sumatra. ITTO and BPTSTH. 42-53. Available online at www.balithut-kuok.org. (In Indonesian). 
    28. Techen, N., Parveen, I., Pan, Z. and Khan, IA. (2014). DNA barcoding of medicinal plant material for identification. Current Opinion Biotechnology. 25: 103-10. 
    29. The Plant List. 2013. http://www.theplantlist.org./ (Accessed November 16, 2019). 
    30. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997). The clustal-X Windows Interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 25: 4876-4882.
    31. Tripathy, S.K., Nayak, P.K. Lenka, D. Swain, D. Baisakh, B. Mohanty, P. Senapati, N. et al. (2016). Morphological diversity of local landraces and wild forms of mungbean. Legume Research-An International Journal. 39: 485-493.
    32. Turland, N.J., Wiersema, J.H., Barrie, F.R., Greuter, W., Hawksworth, D.L., Herendeen, P.S., et al. (2018). International Code of Nomenclature for algae, fungi and plants (Shenzhen Code). Adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books. (Accessed November 16, 2019).
    33. Yusfita, E. (2008). Ethnobotanical Study on Andalas Tree (Morus macroura Miq.). Master Thesis in Dept. Biology, Graduate Faculty andalas University, Padang (In Indonesian). 
    34. Zhang, Y.B. Yuan, Y. Pang, Y.X., Yu, F.L., Yuan, C., Wang, D. Hu, X. (2019). Phylogenetic Reconstruction and Divergence Time Estimation of Blumea DC. (Asteraceae: Inuleae) in China Based on nrDNA ITS and cpDNA trnL-F Sequences. Plants. 8: 1-19.
    35. Zhou, J. Wang, W. Liu, M. and Liu, Z. (2014). Molecular authentication of the traditional medicinal plant Peucedanum praeruptorum and its substitutes and adulterants by DNA-barcoding technique. Pharmacognosy Magazine. 10: 385-390.
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