Indian Journal of Agricultural Research

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Research Article

Indian Journal of Agricultural Research, volume 56 issue 3 (june 2022) : 249-254

Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode

Dang Thanh Long, Hoang Thi Kim Hong, Le Ly Thuy Tram, Nguyen Thi Quynh Trang
1Institute of Biotechnology, Hue University, Provincial Road No. 10, Phu Vang, TTHue, Vietnam.
Cite article:- Long Thanh Dang, Hong Kim Thi Hoang, Tram Thuy Ly Le, Trang Quynh Thi Nguyen (2022). Research on Phylogenetic Relationship of Lotus Populations Collected in Thua Thien Hue Province, Vietnam based on the Chloroplast Genome by DNA Barcode. Indian Journal of Agricultural Research. 56(3): 249-254. doi: 10.18805/IJARe.A-646.

ABSTRACT

Background: The DNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. 
Methods: DNA barcoding of 9 chloroplast genes (rbcL, matK, trnH-psbA, accD-psaI, ndhA, psbE-petL, Rpl32-trnL, trnW-psaJ, trnSGCU-trnGGCC) were used to provide the theoretical basis for species identification, genetic diversity analysis of lotus population collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequence products were analyzed using the MEGA X program.
Result: The results showed that high levels of haplotype diversity (Hd), ranging from 0.618-0.869 and low levels of nucleotide diversity (Pi), ranging from 0.180 × 10-3-3.280 × 10-3 base on a total of nine gene regions of chloroplast genome. The neutrality tests show an excess of rare nucleotide position variations in individuals’ white lotus and derived haplotypes recent expansion. While the evolution of the individuals in the pink lotus may have to decrease. The phylogenetic analyses indicated that combined sequences were not insufficient to make a difference to the DNA barcoding in the individual’s lotus of the N. nucifera species this is in the study. The standardized and accurate barcode information of lotus is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Nelumbonaceae germplasm resources.

REFERENCES


  1. Alam, A., Chadha, N.K., Kumar A.P., Chakraborty, S.K., Joshi, K.D., Sawant, P.B., Das, S.C.S., Kumar, J., Kumar, T. (2020). DNA barcoding and biometric investigation on the invasive oreochromis niloticus (Linnaeus, 1758) from the river Yamuna of Uttar Pradesh. Indian Journal of Animal Research. 54: 856-863.

  2. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. and Saunders N.C. (1987a). Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology, Evolution and Systematics. 18: 489-522.

  3. Chase, M.W., Cowan, R.S., Hollingsworth, P.M., van den Berg, C., Madriñán, S., Petersen, G., Wilkinson, M. (2007). A proposal for a standardized protocol to barcode all land plants. Taxon. 56(2): 295-299. 

  4. Dong, W., Liu, J., Yu, J., Wang, L., Zhou, S. (2012). Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS one. 7(4): e35071. 

  5. Fu, Y.X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147: 915-925.

  6. Fu, Y.X., Li, W.H. (1993). Statistical tests for neutrality of mutations. Genetics. 133: 693-709.

  7. Hartl, D.L., Clark, A.G. (2007). Principles of Population Genetics, 4th edn. Sinauer Associates, Sunderland.

  8. Hedrick, P.W. (2005). A standardized genetic differentiation measure. Evolution. 59(8): 1633-1638. 

  9. Kress, W.J., Erickson, D.L., Jones, F.A., Swenson, N.G., Perez, R., Sanjur, O., Bermingham, E. (2009). Plant DNA Barcodes and a Community Phylogeny of a Tropical Forest Dynamics Plot in Panama. Proceedings of the National Academy of Sciences USA, 106:18621-18626.

  10. Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution. 35: 1547-1549.

  11. Long, D.T., Hong, H.T.K., Tram, L.L.T., Trang, N.T.Q. (2020). Evalution of genetic diversity by dna barcoding of local lotus populations from thua thien hue province. Indian Journal of Agricultural Research. 55(2):121-128.

  12. Maqbool, S., Ullah, N., Zaman, A., Akbar, A., Saeed, S., Nawaz, H., Samad, N., Ullah, R., Bari, A. and Ali, S.S. (2019). Phytochemical screening, in vitro and in vivo anti-diabetic activity of Nelumbo nucifera leaves against alloxan-induced diabetic rabbits. Indian Journal of Animal Research. 54(4): 1-6.

  13. Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., Sánchez-Gracia, A. (2017). DNAsp 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolutio. 34(12): 3299-3302.

  14. Sharma, K., Mishra, A.K., Misra, R.S. (2008). A simple and efficient method for extraction of genomic DNA from tropical tuber crops. African Journal of Biotechnology. 7(8): 1018-1022.

  15. Stroreck, C. (1987). Average number of nucleotide difference in a sample from a single subpopulation: A test for population subdivision. Genetics. 117: 149-153.

  16. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123: 585- 595.

  17. Tamura, K. and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution. 10: 512-526.

  18. 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. 24: 4876- 4882.

  19. Weir, B.S. (1996). Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Inc., Sunderland.

  20. Wright, S. (1984). Evolution and the Genetics of Populations, vol 4: Variability Within and Among Natural Populations. University of Chicago Press.
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