SỬ DỤNG TRÌNH TỰ NUCLEOTIDE VÙNG GEN NHÂN (ITS-rRNA) ĐỂ XÁC ĐỊNH LOÀI LAN THUỘC CHI LAN HOÀNG THẢO (DENDROBIUM)
Nội dung chính của bài viết
Tóm tắt
USING ITS NUCLEAR GENE NUCLEOTIDE SEQUENCES FOR IDENTIFICATION SPECIES IN DENDROBIUM
DNA barcoding is a useful tool for species identification using standardized genomic DNA fragments. We used DNA barcodes (Internal transcribed spacer of the nuclear ribosomal DNA - ITS-rDNA) to explore Dendrobium anosmum, and to investigate the current taxonomy of Dendrobium. In this study, the success rate for PCR of ITS region was 100%. The success rate for bidirectional sequencing of PCR product was 100% with length of 650bp. All 15 samples from two provinces (Hai Duong and Hoa Binh) of Vietnam have close relationship with D. anosmum (MLBS=97%, BPP=100%). Genetic p-distances interspecific divergence within and among Dendrobium species was varied from 1% to 17%, average (12.12%). The genetic relationship of species/gender belonging to the Dendrobium genus showed that they have the same evolutionary origin.
Từ khóa
Dendrobium anosmum, DNA barcoding, DNA Sequencing, identification, ITS (Internal Transcribed Spacer), nhận dạng, DNA mã vạch, lan Phi điệp, trình tự nucleotide
Chi tiết bài viết
Tài liệu tham khảo
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2. Feng S.G., Lu J.J., Gao L., Liu J.J., Wang H.Z., Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China, Biochemical Genetics, 2014, 52:127-136.
3. Tsi Z.H., Chen S.C., Luo Y.B., Zhu G.H., Orchidaceae (3). In flora republicae popularis sinicae, Science Press: Beijing, China, 1999.
4. Adams P.B., Systematics of Dendrobiinae (Orchidaceae), with special reference to Australian taxa, Botanical Journal of the Linnean Society, 2011, 166:105-126.
5. Moudi M., Go R., Yien C.Y.S., Saleh M.N., A review on molecular systematic of the genus Dendrobium Sw, Acta Biologica Malaysiana, 2013, 2(2):71-78
6. Xiang X.G., Schuiteman A., Li D.Z., Huang W.C., Chung S.W., Li J.W., Zhou H.L., Jin W.T., Lai Y.J., Li Z.Y., Jin X.H.., Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences, Molecular Phylogenetics and Evolution, 2013, 69:950-960.
7. Trần Hợp., Phong lan Việt Nam, NXB. Nông nghiệp, Tp. Hồ Chí Minh, 1998.
8. Leonid Averyanov, Anna L. Averyanova., Updated checklist of the Orchids of Vietnam. Vietnam National University Publishing House, Hanoi, 2003.
9. Bulpitt C.J., Li Y., Bulpitt P.F., The use of orchids in Chinese medicine, Journal of the Royal Society of Medicine, 2007, 100(12):558-563.
10. Chinese Pharmmacopoeia Editorial Committee (CPEC). Pharmmacopoeia of the People’s Republic of China. In Theoretical and Applied Genetics, CPEC, Beijing, China, 2010.
11. Jin W., Yao S., Cultivation and appreciation of noble spring Orchid cultivars; Guangdong Science and Technology Press: Guangzhou, China, 2006.
12. Trung K.H., Khanh T.D., Ham L.H., Duong T.D., Khoa N.T., Molecular phylogeny of the endangered Vietnamese Paphiopedilum species based on the internal transcribed spacer of the nuclear ribosomal DNA, Advanced Studies in Biology, 2013, 5:337-346. 13. Ding G., Li X., Ding X., Qian L., Genetic diversity across natural populations of Dendrobium officinale, the endangered medicinal herb endemic to China, revealed by ISSR and RAPD markers, Genetika, 2009, 45:375-382.
14. Lau D.T., Shaw P.C., Wang J., But P.P., Authentication of medicinal Dendrobium species by the internal transcribed spacer of ribosomal DNA, Planta Medica, 2001, 67:456-460.
15. Feng S., He R., Yang S., Chen Z., Jiang M., Lu J., Wang H., Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species, Gene, 2015, 567:182-188.
16. Hebert P.D.N., Penton E.H., Burns J.M., Janzen D.H., Hallwachs W., Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator, Proceedings of the National Academy of Sciences of the United States of America, 2004, 101:14812-14817.
17. Liu J., Provan J., Gao L.M., Li D.Z., Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: A case study in taxus, International Journal of Molecular Sciences, 2012a, 13:8740-8751.
18. Chen S., Yao H., Han J., Liu, C., Song J., Shi L., Zhu Y., Ma X., Gao T., Pang X., Luo K., Li Y., Li X., Jia X., Lin Y., Leon C., Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species, PLoS ONE, 2010, 5:e8613.
19. Gao T., Yao H., Song J., Liu C., Zhu Y., Ma X., Pang X., Xu H., Chen S., Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2, Journal of Ethnopharmacology, 2010, 130:116-121
20. Liu Z., Zeng X., Yang D., Ren G., Chu G., Yuan Z., Luo K., Xiao P., Chen S., Identification of medicinal vines by ITS2 using complementary discrimination methods. Journal of Ethnopharmacology, 2012b, 141:242-249.
21. Yao H., Song J.Y., Ma X.Y., Liu C., Li Y., Xu H.X., Han J.P., Duan L.S., Chen S.L., Identification of Dendrobium Species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region. Planta Medica, 2009, 75:667-669.
22. Kress W.J., Erickson D.L., A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region, PLoS ONE 2007, 2:e508.
23. Lahaye R., van der Bank M., Bogarin D., Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S. Barraclough T.G., Savolainen V., DNA barcoding the floras of biodiversity hotspots, Proceedings of the National Academy of Sciences of the United States of America, 2008, 105:2923-2928.
24. Kumar P., Rawat G.S., Wood H.P., Diversity and ecology of Dendrobiums (Orchidaceae) in Chotanagpur plateau, India, Taiwania, 2011, 56(1):23-36.
25. Sharma S.K., Dkhar J., Kumaria S., Tandon P., Rao S.R., Assessment of phylogenetic inter-relationships in the genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA, Gene, 2012, 495:10-15.
26. Peyachoknagul S., Nettuwakul C., Phuekvilai P., Wannapinpong S., Srikulnath K., Development of microsatellite markers of vandaceous orchids for species and variety identification, Genetics and Molecular Research, 2014, 13:5441-5445.
27. Chen W.H., Kao Y.L., Tang C.Y., Tsai C.C., Lin T.Y., Estimating nuclear DNA content within 50 species of the genus Phalaenopsis Blume (Orchidaceae), Scientia Horticulture, 2013, 161:70-75.
28. Tran Duy Duong, Khuat Huu Trung, La Tuan Nghia, Nguyen Thi Thanh Thuy, Pham Bich Hien, Nguyen Truong Khoa, Tran Hoang Dung, Do Minh Trung, Tran Dang Khanh, Identification of Vietnamese native Dendrobium species based on ribosomal DNA internal transcribed spacer sequence, Advanced Studies in Biology, 2018, 10(1):1-12
29. Liu Y.T., Chen R.K., Lin S.J., Chen Y.C., Chin S.W., Chen F.C., Lee C.Y., Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species, Genetics and Molecular Research, 2014, 13(2):2709-2717.
30. Burke J.M., Bayly M.J., Adams P.B., Ladiges P.Y., Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification, Australian Systematic Botany, 2008, 21:1-14
31. Yukawa T., Uehara K., Vegetative diversification and radiation in subtribe Dendrobiinae (Orchidaceae):Evidence from chloroplast DNA phylogeny and anatomical characters, Plant Systematics and Evolution, 1996, 201:1-14
32. Morris M.W., Steen W.L., Judd W.S., Vegetative anatomy and systematics of subtribe Dendrobiinae (Orchidaceae), Botanical Journal of the Linnean Society, 1996, 120:89-144.
33. Blasi A.T., Vorontsova M., Plant identification is key to conservation, Nature, 2015, 521:161
34. Burke J.M., Bayly M.J., Adams P.B., Ladiges P.Y., Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification, Australian Systematic Botany, 2008, 21:1-14
35. Schuiteman A., Dendrobium (Orchidaceae): To split or not split, Gard Bull Singapore, 2011, 63:245-257.
36. Tsai C.C., Chiang Y.C., Huang S.C., Chen C.H., Chou C.H., Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) on the basis of plastid and nuclear DNA, Plant Systematics and Evolution, 2010, 288:77-98.
37. Chromas Pro2.1.6 (Technelysium Pty Ltd, Helensvale, Queensland, Australia)
38. Hall T.A., 1999. BioEdit v7.0.5.2: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symposium Series, 1999, 41:95-98
39. Jobb G., TREEFINDER version March 2011. http://www.treefinder.de
40. Ronquist F., Huelsenbeck J.P, MrBAYES 2.3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 2003, 19:1572-1574
41.Tanabe A.S., Kakusan 4 and Aminosan: two programs for comparing
nonpartitioned, proportional and separate models for combined molecular
phylogenetic analyses of multilocus sequence data. Molecular Ecology Resources, 2011, 11:914-921.
42. Rambaut A., Drummond A., TRACER version 1.5, 2009 http://beast.bio.ed.ac.uk/Tracer
43. Huelsenbeck J.P., Hillis D.M., 1993. Success of phylogenetic methods in the fourtaxon case, Systematic Biology, 1993, 42:247-264.
44. Leaché A.D., Reeder T.W., Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches, Systematic Biology, 2002, 51:44-68.
45. Kumar S., Stecher G., Tamura K., MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets, Molecular Biology and Evolution, 2016, 33(7):1870-1874.
46. Dương Văn Tăng, Nguyễn Quốc Bình, Đinh Thị Phòng, Trình tự nucleotide vùng ITS nhân và mối quan hệ di truyền của 3 loài gỗ quý Việt Nam: Trắc (Dalbergia cochinchinensis), Cẩm lai (D. oliveri) và Sưa (D. tonkinensis). Hội nghị Khoa học Toàn quốc về Sinh thái và Tài nguyên sinh vật lần thứ 4, 2011, tr.1296-1300.
2. Feng S.G., Lu J.J., Gao L., Liu J.J., Wang H.Z., Molecular phylogeny analysis and species identification of Dendrobium (Orchidaceae) in China, Biochemical Genetics, 2014, 52:127-136.
3. Tsi Z.H., Chen S.C., Luo Y.B., Zhu G.H., Orchidaceae (3). In flora republicae popularis sinicae, Science Press: Beijing, China, 1999.
4. Adams P.B., Systematics of Dendrobiinae (Orchidaceae), with special reference to Australian taxa, Botanical Journal of the Linnean Society, 2011, 166:105-126.
5. Moudi M., Go R., Yien C.Y.S., Saleh M.N., A review on molecular systematic of the genus Dendrobium Sw, Acta Biologica Malaysiana, 2013, 2(2):71-78
6. Xiang X.G., Schuiteman A., Li D.Z., Huang W.C., Chung S.W., Li J.W., Zhou H.L., Jin W.T., Lai Y.J., Li Z.Y., Jin X.H.., Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences, Molecular Phylogenetics and Evolution, 2013, 69:950-960.
7. Trần Hợp., Phong lan Việt Nam, NXB. Nông nghiệp, Tp. Hồ Chí Minh, 1998.
8. Leonid Averyanov, Anna L. Averyanova., Updated checklist of the Orchids of Vietnam. Vietnam National University Publishing House, Hanoi, 2003.
9. Bulpitt C.J., Li Y., Bulpitt P.F., The use of orchids in Chinese medicine, Journal of the Royal Society of Medicine, 2007, 100(12):558-563.
10. Chinese Pharmmacopoeia Editorial Committee (CPEC). Pharmmacopoeia of the People’s Republic of China. In Theoretical and Applied Genetics, CPEC, Beijing, China, 2010.
11. Jin W., Yao S., Cultivation and appreciation of noble spring Orchid cultivars; Guangdong Science and Technology Press: Guangzhou, China, 2006.
12. Trung K.H., Khanh T.D., Ham L.H., Duong T.D., Khoa N.T., Molecular phylogeny of the endangered Vietnamese Paphiopedilum species based on the internal transcribed spacer of the nuclear ribosomal DNA, Advanced Studies in Biology, 2013, 5:337-346. 13. Ding G., Li X., Ding X., Qian L., Genetic diversity across natural populations of Dendrobium officinale, the endangered medicinal herb endemic to China, revealed by ISSR and RAPD markers, Genetika, 2009, 45:375-382.
14. Lau D.T., Shaw P.C., Wang J., But P.P., Authentication of medicinal Dendrobium species by the internal transcribed spacer of ribosomal DNA, Planta Medica, 2001, 67:456-460.
15. Feng S., He R., Yang S., Chen Z., Jiang M., Lu J., Wang H., Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species, Gene, 2015, 567:182-188.
16. Hebert P.D.N., Penton E.H., Burns J.M., Janzen D.H., Hallwachs W., Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator, Proceedings of the National Academy of Sciences of the United States of America, 2004, 101:14812-14817.
17. Liu J., Provan J., Gao L.M., Li D.Z., Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: A case study in taxus, International Journal of Molecular Sciences, 2012a, 13:8740-8751.
18. Chen S., Yao H., Han J., Liu, C., Song J., Shi L., Zhu Y., Ma X., Gao T., Pang X., Luo K., Li Y., Li X., Jia X., Lin Y., Leon C., Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species, PLoS ONE, 2010, 5:e8613.
19. Gao T., Yao H., Song J., Liu C., Zhu Y., Ma X., Pang X., Xu H., Chen S., Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2, Journal of Ethnopharmacology, 2010, 130:116-121
20. Liu Z., Zeng X., Yang D., Ren G., Chu G., Yuan Z., Luo K., Xiao P., Chen S., Identification of medicinal vines by ITS2 using complementary discrimination methods. Journal of Ethnopharmacology, 2012b, 141:242-249.
21. Yao H., Song J.Y., Ma X.Y., Liu C., Li Y., Xu H.X., Han J.P., Duan L.S., Chen S.L., Identification of Dendrobium Species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region. Planta Medica, 2009, 75:667-669.
22. Kress W.J., Erickson D.L., A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region, PLoS ONE 2007, 2:e508.
23. Lahaye R., van der Bank M., Bogarin D., Warner J., Pupulin F., Gigot G., Maurin O., Duthoit S. Barraclough T.G., Savolainen V., DNA barcoding the floras of biodiversity hotspots, Proceedings of the National Academy of Sciences of the United States of America, 2008, 105:2923-2928.
24. Kumar P., Rawat G.S., Wood H.P., Diversity and ecology of Dendrobiums (Orchidaceae) in Chotanagpur plateau, India, Taiwania, 2011, 56(1):23-36.
25. Sharma S.K., Dkhar J., Kumaria S., Tandon P., Rao S.R., Assessment of phylogenetic inter-relationships in the genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA, Gene, 2012, 495:10-15.
26. Peyachoknagul S., Nettuwakul C., Phuekvilai P., Wannapinpong S., Srikulnath K., Development of microsatellite markers of vandaceous orchids for species and variety identification, Genetics and Molecular Research, 2014, 13:5441-5445.
27. Chen W.H., Kao Y.L., Tang C.Y., Tsai C.C., Lin T.Y., Estimating nuclear DNA content within 50 species of the genus Phalaenopsis Blume (Orchidaceae), Scientia Horticulture, 2013, 161:70-75.
28. Tran Duy Duong, Khuat Huu Trung, La Tuan Nghia, Nguyen Thi Thanh Thuy, Pham Bich Hien, Nguyen Truong Khoa, Tran Hoang Dung, Do Minh Trung, Tran Dang Khanh, Identification of Vietnamese native Dendrobium species based on ribosomal DNA internal transcribed spacer sequence, Advanced Studies in Biology, 2018, 10(1):1-12
29. Liu Y.T., Chen R.K., Lin S.J., Chen Y.C., Chin S.W., Chen F.C., Lee C.Y., Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species, Genetics and Molecular Research, 2014, 13(2):2709-2717.
30. Burke J.M., Bayly M.J., Adams P.B., Ladiges P.Y., Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification, Australian Systematic Botany, 2008, 21:1-14
31. Yukawa T., Uehara K., Vegetative diversification and radiation in subtribe Dendrobiinae (Orchidaceae):Evidence from chloroplast DNA phylogeny and anatomical characters, Plant Systematics and Evolution, 1996, 201:1-14
32. Morris M.W., Steen W.L., Judd W.S., Vegetative anatomy and systematics of subtribe Dendrobiinae (Orchidaceae), Botanical Journal of the Linnean Society, 1996, 120:89-144.
33. Blasi A.T., Vorontsova M., Plant identification is key to conservation, Nature, 2015, 521:161
34. Burke J.M., Bayly M.J., Adams P.B., Ladiges P.Y., Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification, Australian Systematic Botany, 2008, 21:1-14
35. Schuiteman A., Dendrobium (Orchidaceae): To split or not split, Gard Bull Singapore, 2011, 63:245-257.
36. Tsai C.C., Chiang Y.C., Huang S.C., Chen C.H., Chou C.H., Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) on the basis of plastid and nuclear DNA, Plant Systematics and Evolution, 2010, 288:77-98.
37. Chromas Pro2.1.6 (Technelysium Pty Ltd, Helensvale, Queensland, Australia)
38. Hall T.A., 1999. BioEdit v7.0.5.2: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symposium Series, 1999, 41:95-98
39. Jobb G., TREEFINDER version March 2011. http://www.treefinder.de
40. Ronquist F., Huelsenbeck J.P, MrBAYES 2.3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 2003, 19:1572-1574
41.Tanabe A.S., Kakusan 4 and Aminosan: two programs for comparing
nonpartitioned, proportional and separate models for combined molecular
phylogenetic analyses of multilocus sequence data. Molecular Ecology Resources, 2011, 11:914-921.
42. Rambaut A., Drummond A., TRACER version 1.5, 2009 http://beast.bio.ed.ac.uk/Tracer
43. Huelsenbeck J.P., Hillis D.M., 1993. Success of phylogenetic methods in the fourtaxon case, Systematic Biology, 1993, 42:247-264.
44. Leaché A.D., Reeder T.W., Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches, Systematic Biology, 2002, 51:44-68.
45. Kumar S., Stecher G., Tamura K., MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets, Molecular Biology and Evolution, 2016, 33(7):1870-1874.
46. Dương Văn Tăng, Nguyễn Quốc Bình, Đinh Thị Phòng, Trình tự nucleotide vùng ITS nhân và mối quan hệ di truyền của 3 loài gỗ quý Việt Nam: Trắc (Dalbergia cochinchinensis), Cẩm lai (D. oliveri) và Sưa (D. tonkinensis). Hội nghị Khoa học Toàn quốc về Sinh thái và Tài nguyên sinh vật lần thứ 4, 2011, tr.1296-1300.