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Comparative Analysis of Different DNA Extraction Methods and Preliminary Analysis of Genetic Diversity of Hedera nepalensis K. Koch. in Vietnam Based on GBSSI Marker
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Though the ivy (Hedera nepalensis K. Koch.) has long been utilized in traditional medicine, its genome information is very limited. For plants, an effective method of DNA extraction is a very important step which greatly affects subsequent genetic analyses. In this study, four different methods of DNA extraction from dry leaves were used. A comparison of different protocols resulted in the yield of extracted DNA that ranged from 10.5 to 437.4 ng/μl and with a purity ranged from 1.8 to 2.2. Based on the PCR results of GBSSI gene, Gene JET Plant Genomic DNA Purification Mini Kit is the most optimal extraction method for Vietnam ivy’s dry leaves. A preliminary analysis of the phylogenetic tree based on the GBSSI marker showed that ivy growing in a number of northern mountainous provinces of Vietnam belonged to the H. nepalensis K. Koch species. The high - quality total DNA will allow us to amplify different DNA markers, providing valuable genetic information to preserve and develop medicinal resources in Vietnam.
Keywords
GBSSI, Hedera nepalensis K. Koch, DNA extraction.
References
[1] J. Ackerfield, J. Wen, A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications, Adansonia Sér. 24 (2002) 187-212.[2] U.S. National Plant Germplasm System, Taxon: Hedera nepalensis K. Koch, https://npgsweb.ars -grin.gov/gringlobal/taxonomydetail.aspx?id= 18567, 2019 (accessed 21 March 2019). [3] L. Jafri, S. Saleem, T.P. Kondrytuk, I.Q. Haq, N. Ullah, J.M. Pezzuto, B. Mirza, Hedera nepalensis K. Koch: A Novel Source of Natural Cancer Chemopreventive and Anticancerous Compounds, Phytotherapy Reserch. 30 (2016) 447-453.[4] S. Saleem, L. Jafri, I. Haq, L.C. Chang, D. Calderwood, B.D. Green, B. Mirza, Plants Fagonia cretica L. and Hedera nepalensis K. Koch contain natural compounds with potent dipeptidyl peptidase-4 (DPP-4) inhibitory activity, Journal of Ethnopharmacology. 156 (2014) 26-32.[5] W.J. Hashmi, H. Ismail, F. Mehmood, B. Mirza, Neuroprotective, antidiabetic and antioxidant effect of Hedera nepalensis and lupeol against STZ+ AlCl3 induced rats model, DARU: Journal of faculty of Pharmacy, Tehran University of Medical Sciences. 26 (2018) 179-190.[6] H. Ismail, A. Rasheed, I.U. Haq, L. Jafri, N. Ullah, E. Dilshad, M. Sajd, B. Mirza, Five indigenous plants of Pakistan with Antinociceptive, anti-inflammatory, antidepressant, and anticoagulant properties in Sprague Dawley rats, Evidence-based Complementary and alternative medicine 2017 (2017) 1-10.[7] A. Mitchell, J. Wen. Phylogenetic utility and evidence for multiple copies of granule-bound starch synthase I (GBSSI) in Araliaceae, Taxon 53 (2004) 29-44.[8] M.A. Saghai-Maroof, K.M. Soliman, R.A. Jorgensen, R.W.L. Allard, Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics, Proceeding of the National Academy of Sciences of the USA. 81 (1984) 8014-8018.[9] M. Elias, G.S. Mühlen, D. McKey, A.C. Roa, J. Tohme, Genetic diversity of traditional South American landraces of cassava (Manihot esculenta Crantz): an analysis using microsatellites, Economic Botany. 58 (2004) 242-256.[10] B.D. Lade, A.S. Patil, H.M. Paikrao, Efficient genomic DNA extraction protocol from medicinal rich Passiflora foetida containing high level of polysaccharide and polyphenol, Springerplus. 3 (2014) 1-7.[11] J.H. Cota-Sánchez, K. Remarchuk, K. Ubayasena, Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue, Plant Molecular Biology Reporter. 24 (2006) 161.[12] J. Zhang, J.M. Stewart, Economical and rapid method for extracting cotton genomic DNA, Journal of Cotton Science. 4 (2000) 193-201.[13] T. Li, H. Pan, Y. Feng, H. Li, Y. Zhao, Bioactivity-guided isolation of anticancer constituents from Hedera nepalensis K. Koch, South African Journal of Botany. 100 (2015) 87-93.[14] L. Jafri, S. Saleem, N. Ullah, B. Mirza, In vitro assessment of antioxidant potential and determination of polyphenolic compounds of Hedera nepalensis K. Koch, Arabian Journal of Chemistry. 10 (2017) S3699-S3706.[15] B. Ahmad, N. Munir, S. Bashir, S. Azam, I. Khan, M. Ayub, Biological screening of Hedera nepalensis, Journal of Medicinal Plants Research. 6 (2012) 5250-5257.[16] K.H.E. Koch, Hortus Dendrologicus, F. Schneider & Co., Berlin, 1985, pp 250.[17] A. Rehder, New species, varieties and combinations from the herbarim and the collections of the Arnold arboretum, Journal of the Arnold Arboretum. 4 (1923) 250.
Vietnam National University Journal of Science
Title: Comparative Analysis of Different DNA Extraction Methods and Preliminary Analysis of Genetic Diversity of Hedera nepalensis K. Koch. in Vietnam Based on GBSSI Marker
Description:
Though the ivy (Hedera nepalensis K.
Koch.
) has long been utilized in traditional medicine, its genome information is very limited.
For plants, an effective method of DNA extraction is a very important step which greatly affects subsequent genetic analyses.
In this study, four different methods of DNA extraction from dry leaves were used.
A comparison of different protocols resulted in the yield of extracted DNA that ranged from 10.
5 to 437.
4 ng/μl and with a purity ranged from 1.
8 to 2.
2.
Based on the PCR results of GBSSI gene, Gene JET Plant Genomic DNA Purification Mini Kit is the most optimal extraction method for Vietnam ivy’s dry leaves.
A preliminary analysis of the phylogenetic tree based on the GBSSI marker showed that ivy growing in a number of northern mountainous provinces of Vietnam belonged to the H.
nepalensis K.
Koch species.
The high - quality total DNA will allow us to amplify different DNA markers, providing valuable genetic information to preserve and develop medicinal resources in Vietnam.
Keywords
GBSSI, Hedera nepalensis K.
Koch, DNA extraction.
References
[1] J.
Ackerfield, J.
Wen, A morphometric analysis of Hedera L.
(the ivy genus, Araliaceae) and its taxonomic implications, Adansonia Sér.
24 (2002) 187-212.
[2] U.
S.
National Plant Germplasm System, Taxon: Hedera nepalensis K.
Koch, https://npgsweb.
ars -grin.
gov/gringlobal/taxonomydetail.
aspx?id= 18567, 2019 (accessed 21 March 2019).
[3] L.
Jafri, S.
Saleem, T.
P.
Kondrytuk, I.
Q.
Haq, N.
Ullah, J.
M.
Pezzuto, B.
Mirza, Hedera nepalensis K.
Koch: A Novel Source of Natural Cancer Chemopreventive and Anticancerous Compounds, Phytotherapy Reserch.
30 (2016) 447-453.
[4] S.
Saleem, L.
Jafri, I.
Haq, L.
C.
Chang, D.
Calderwood, B.
D.
Green, B.
Mirza, Plants Fagonia cretica L.
and Hedera nepalensis K.
Koch contain natural compounds with potent dipeptidyl peptidase-4 (DPP-4) inhibitory activity, Journal of Ethnopharmacology.
156 (2014) 26-32.
[5] W.
J.
Hashmi, H.
Ismail, F.
Mehmood, B.
Mirza, Neuroprotective, antidiabetic and antioxidant effect of Hedera nepalensis and lupeol against STZ+ AlCl3 induced rats model, DARU: Journal of faculty of Pharmacy, Tehran University of Medical Sciences.
26 (2018) 179-190.
[6] H.
Ismail, A.
Rasheed, I.
U.
Haq, L.
Jafri, N.
Ullah, E.
Dilshad, M.
Sajd, B.
Mirza, Five indigenous plants of Pakistan with Antinociceptive, anti-inflammatory, antidepressant, and anticoagulant properties in Sprague Dawley rats, Evidence-based Complementary and alternative medicine 2017 (2017) 1-10.
[7] A.
Mitchell, J.
Wen.
Phylogenetic utility and evidence for multiple copies of granule-bound starch synthase I (GBSSI) in Araliaceae, Taxon 53 (2004) 29-44.
[8] M.
A.
Saghai-Maroof, K.
M.
Soliman, R.
A.
Jorgensen, R.
W.
L.
Allard, Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics, Proceeding of the National Academy of Sciences of the USA.
81 (1984) 8014-8018.
[9] M.
Elias, G.
S.
Mühlen, D.
McKey, A.
C.
Roa, J.
Tohme, Genetic diversity of traditional South American landraces of cassava (Manihot esculenta Crantz): an analysis using microsatellites, Economic Botany.
58 (2004) 242-256.
[10] B.
D.
Lade, A.
S.
Patil, H.
M.
Paikrao, Efficient genomic DNA extraction protocol from medicinal rich Passiflora foetida containing high level of polysaccharide and polyphenol, Springerplus.
3 (2014) 1-7.
[11] J.
H.
Cota-Sánchez, K.
Remarchuk, K.
Ubayasena, Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue, Plant Molecular Biology Reporter.
24 (2006) 161.
[12] J.
Zhang, J.
M.
Stewart, Economical and rapid method for extracting cotton genomic DNA, Journal of Cotton Science.
4 (2000) 193-201.
[13] T.
Li, H.
Pan, Y.
Feng, H.
Li, Y.
Zhao, Bioactivity-guided isolation of anticancer constituents from Hedera nepalensis K.
Koch, South African Journal of Botany.
100 (2015) 87-93.
[14] L.
Jafri, S.
Saleem, N.
Ullah, B.
Mirza, In vitro assessment of antioxidant potential and determination of polyphenolic compounds of Hedera nepalensis K.
Koch, Arabian Journal of Chemistry.
10 (2017) S3699-S3706.
[15] B.
Ahmad, N.
Munir, S.
Bashir, S.
Azam, I.
Khan, M.
Ayub, Biological screening of Hedera nepalensis, Journal of Medicinal Plants Research.
6 (2012) 5250-5257.
[16] K.
H.
E.
Koch, Hortus Dendrologicus, F.
Schneider & Co.
, Berlin, 1985, pp 250.
[17] A.
Rehder, New species, varieties and combinations from the herbarim and the collections of the Arnold arboretum, Journal of the Arnold Arboretum.
4 (1923) 250.
.
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