Araştırma Makalesi


DOI :10.26650/EurJBiol.2024.1447284   IUP :10.26650/EurJBiol.2024.1447284    Tam Metin (PDF)

Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu

Nguyen Trung QuanHoang Thanh ChiPhung My TrungTruong Quang CuongTran Thi Cam ThiHoang Kim SonBui Thi Kim Ly

Objective: Theaceae is a commodity with high economic value. The diversity of Theaceae species present in Southeast Asia, especially Vietnam, provides an excellent supply source for promoting the development of related industries. Nearly 130 species of Theaceae, many of which are highly endemic, were discovered in Vietnam, including 13 Polyspora species. Polyspora huongiana was discovered in Bidoup-Nui Ba National Park, Vietnam, on January 7, 2010. Because they are native species and lack data, studies are needed to provide genetic data for ecological assessment and original identification of the plant.

Materials and Methods: Sanger sequencing, data collection, and nucleotide analysis of the genetic data of accD, matK, rbcL, and ycf1 in P. huongiana were provided.

Results: The results showed that combinations of two sequences could separate the Polyspora genus, whereas at least three sequences were necessary to identify P. huongiana, which was genetically closely related to Polyspora axillaris and Polyspora hainanensis.

Conclusion: P. huongiana is closely related to Polyspora axillaris and Hainanensis. The combination of 3–4 sequences allowed reliable identification of P. huongiana.

Anahtar Kelimeler: Polyspora huongianaPhylogenymatKrbcLaccDycf1

PDF Görünüm

Referanslar

  • 1. Nguyet Hai Ninh L, Luong V, Nguyen Van C, et al. An updated checklist of Theaceae and a new species of Polyspora from Vietnam. Taiwania. 2020;65(2):216-227. google scholar
  • 2. Dung LV, Lieu NT, Cuong TQ, Thanh NT. Da tu tra la nho (Polyspora microphylla Luong, Nguyen et Truong) mot loai moi thuoc ho Ch (Theaceae) o Viet Nam. JS: NST. 2016;32(2):1-5. google scholar
  • 3. Orel G, Wilson PG, Curry AS, Luu HT. Polyspora huongiana sp. nov. (Theaceae) from Vietnam and notes on related species. Nord J Bot. 2012;30(1):47-52. google scholar
  • 4. Beech E, Barstow M, Rivers M. The Red List of Theaceae. 2017. google scholar
  • 5. Le S, Lesueur D, Herrmann L, et al. Sustainable tea production through agroecological management practices in Vietnam: A re-view. J Environ Sustain. 2021;4:589-604. google scholar
  • 6. Romprasert S. Sweet green tea consumption with health eco-nomics matter. Int J Econ Res. 2017;14:193-202. google scholar
  • 7. Zhang W, Kan S-l, Zhao H, Li Z-y, Wang X-q. Molecu-lar phylogeny of Tribe theeae (Theaceae s.s.) and its implica-tions for generic delimitation. PLoS One. 2014;9(5):e98133. doi: 10.1371/journal.pone.0098133 google scholar
  • 8. Cheng L, Li M, Han Q, et al. Phylogenomics resolves the phy-logeny of Theaceae by using low-copy and multi-copy nuclear gene makers and uncovers a fast radiation event contributing to tea plants diversity. Biology (Basel). 2022;11(7). doi: 10.3390/bi-ology11071007 google scholar
  • 9. Fan Z-F, Ma C-L. Comparative chloroplast genome and phyloge-netic analyses of Chinese Polyspora. Sci Rep. 2022;12(1):15984. doi: 10.1038/s41598-022-16290-4 google scholar
  • 10. Erdei B, Hably L. Fossil Gordonia (s.l.)-like (Theaceae) winged seeds from the early Miocene of the Mecsek Mts, W Hungary. Paleobiodivers Paleoenviron. 2021;101(1):59-67. google scholar
  • 11. Sucher N, Hennell J, Carles M. DNA Fingerprinting, DNA bar-coding, and next generation sequencing technology in plants. Methods Mol Biol. 2012;862:13-22. google scholar
  • 12. Ankola K, Mahadevegowda L, Melichar T, Boregowda MH. Chapter 18 - DNA barcoding: nucleotide signature for identifi-cation and authentication of livestock. In: Mondal S, Singh RL, editors. Advances in Animal Genomics: Academic Press; 2021. p. 299-308. google scholar
  • 13. Kress W, Erickson D. DNA Barcodes: Methods and Protocols. Methods Mol Biol. 2012;858:3-8. google scholar
  • 14. Orel G, Wilson PG, Curry AS, Luu HT. Polyspora huongiana sp. nov. (Theaceae) from Vietnam and notes on related species. Nord J Bot. 2012;30(1):47-52. google scholar
  • 15. Huang H, Shi C, Liu Y, Mao SY, Gao LZ. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: Genome structure and phylogenetic rela-tionships. BMC Evol Biol. 2014;14:151. doi: 10.1186/1471-2148-14-151 google scholar
  • 16. Li W, Zhang C, Guo X, Liu Q, Wang K. Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis. PLoS One. 2019;14(5):e0216645-e. doi: 10.1371/journal.pone.0216645 google scholar
  • 17. Aboul-Maaty NA-F, Oraby HA-S. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. BNRC. 2019;43(1):25. doi: 10.1186/s42269-019-0066-1 google scholar
  • 18. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evo-lutionary Genetics Analysis Version 11. Mol Biol Evol. 2021;38(7):3022-3027. doi: 10.1093/molbev/msab120 google scholar
  • 19. Rozas J, Ferrer-Mata A, Sanchez-DelBamo JC, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34(12):3299-3302. google scholar
  • 20. Ho VT, Tran TKP, Vu TTT, Widiarsih S. Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam. J Genet Eng Biotechnol. 2021;19(1):93. doi: 10.1186/s43141-021-00188-1 google scholar
  • 21. Saitou N, Nei M. The neighbor-joining A new method for recon-structing phylogenetic trees. Mol Biol Evol. 1987;4(4):406-425. google scholar
  • 22. Wang Y, Yao X, Liu R, Liu C. DDQR (dynamic DNA QR coding): An efficient algorithm to represent DNA barcode sequences. PLoS One. 2023;18(1):e0279994. doi: 10.1371/journal.pone.0279994 google scholar
  • 23. Li Q, Guo Q, Gao C, Li H. Characterization of complete chloro-plast genome of Camellia weiningensis in Weining, Guizhou Province. J Acta Horticulturae Sinica. 2020;47:779-787. google scholar
  • 24. Zheng H, Wei S. Complete chloroplast genomes of Camellia pubipetala Y. Wan et S. Z. Huang and Camellia debaoensis R. C. Hu et Y. Q. Liufu. Mitochondrial DNA B Resour. 2021;6(8):2381-2382. google scholar
  • 25. Yu XQ, Gao LM, Soltis DE, et al. Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family. New Phytol. 2017;215(3):1235-1248. google scholar
  • 26. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol. 1992;9(4):678-687. google scholar
  • 27. Buckley TR, Simon C, Chambers GK. Exploring among-site rate variation models in a maximum likelihood framework us-ing empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst Biol. 2001;50(1):67-86. google scholar
  • 28. Wei S-J, Liufu Y-Q, Zheng H-W, et al. Using phylogenomics to un-tangle the taxonomic incongruence of yellow-flowered Camellia species (Theaceae) in China. J Syst Evol. 2023;61(5):748-763. google scholar
  • 29. Enan M, Al-Deeb M, Fawzi N, Amiri K. DNA Barcoding of Ricinus communis from different geographical origin by using chloroplast matk and internal transcribed spacers. Am J Plant Sci. 2012;03:1304-1310. google scholar
  • 30. Kang Y, Deng Z, Zang R, Long W. DNA barcoding analysis and phylogenetic relationships of tree species in tropical cloud forests. Sci Rep. 2017;7(1):12564. doi: 10.1038/s41598-017-13057-0 google scholar
  • 31. Patwardhan A, Ray S, Roy A. Molecular Markers in Phyloge-netic studies-A review. J Phylogen Evolution Biol. 2014;2:2. doi: 10.4172/2329-9002.1000131 google scholar
  • 32. Meyer CP, Paulay G. DNA barcoding: Error rates based on comprehensive sampling. PLoS Biol. 2005;3(12):e422. doi: 10.1371/journal.pbio.0030422 google scholar
  • 33. Liao M, Gao X, Zhang J, Deng H-N, Xu B. Comparative chloroplast genomics of Sophora species: Evolution and phy-logenetic relationships in the early-diverging legume subfamily Papilionoideae (Fabaceae). Front Plant Sci. 2021;12:778933. doi: 10.3389/fpls.2021.778933 google scholar
  • 34. Li H, Xiao W, Tong T, et al. The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants. Sci Rep. 2021;11(1):1424. doi: 10.1038/s41598-021-81087-w google scholar
  • 35. Birch JL, Walsh NG, Cantrill DJ, Holmes GD, Murphy DJ. Test-ing efficacy of distance and tree-based methods for DNA bar-coding of grasses (Poaceae tribe Poeae) in Australia. PLoS One. 2017;12(10):e0186259. doi: 10.1371/journal.pone.0186259 google scholar
  • 36. Hebert PD, Cywinska A, Ball SL, deWaard JR. Biolog-ical identifications through DNA barcodes. Proc Biol Sci. 2003;270(1512):313-321. google scholar
  • 37. Abbas A, Ali A, Hussain A, et al. Assessment of genetic variability and evolutionary relationships of Rhizoctonia solani inherent in legume crops. Plants. 2023;12(13):2515. doi: 10.3390/plants12132515 google scholar

Atıflar

Biçimlendirilmiş bir atıfı kopyalayıp yapıştırın veya seçtiğiniz biçimde dışa aktarmak için seçeneklerden birini kullanın


DIŞA AKTAR



APA

Quan, N.T., Chi, H.T., My Trung, P., Cuong, T.Q., Thi, T.T., Son, H.K., & Ly, B.T. (2024). Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu. European Journal of Biology, 0(0), -. https://doi.org/10.26650/EurJBiol.2024.1447284


AMA

Quan N T, Chi H T, My Trung P, Cuong T Q, Thi T T, Son H K, Ly B T. Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu. European Journal of Biology. 2024;0(0):-. https://doi.org/10.26650/EurJBiol.2024.1447284


ABNT

Quan, N.T.; Chi, H.T.; My Trung, P.; Cuong, T.Q.; Thi, T.T.; Son, H.K.; Ly, B.T. Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu. European Journal of Biology, [Publisher Location], v. 0, n. 0, p. -, 2024.


Chicago: Author-Date Style

Quan, Nguyen Trung, and Hoang Thanh Chi and Phung My Trung and Truong Quang Cuong and Tran Thi Cam Thi and Hoang Kim Son and Bui Thi Kim Ly. 2024. “Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu.” European Journal of Biology 0, no. 0: -. https://doi.org/10.26650/EurJBiol.2024.1447284


Chicago: Humanities Style

Quan, Nguyen Trung, and Hoang Thanh Chi and Phung My Trung and Truong Quang Cuong and Tran Thi Cam Thi and Hoang Kim Son and Bui Thi Kim Ly. Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu.” European Journal of Biology 0, no. 0 (Nov. 2024): -. https://doi.org/10.26650/EurJBiol.2024.1447284


Harvard: Australian Style

Quan, NT & Chi, HT & My Trung, P & Cuong, TQ & Thi, TT & Son, HK & Ly, BT 2024, 'Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu', European Journal of Biology, vol. 0, no. 0, pp. -, viewed 8 Nov. 2024, https://doi.org/10.26650/EurJBiol.2024.1447284


Harvard: Author-Date Style

Quan, N.T. and Chi, H.T. and My Trung, P. and Cuong, T.Q. and Thi, T.T. and Son, H.K. and Ly, B.T. (2024) ‘Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu’, European Journal of Biology, 0(0), pp. -. https://doi.org/10.26650/EurJBiol.2024.1447284 (8 Nov. 2024).


MLA

Quan, Nguyen Trung, and Hoang Thanh Chi and Phung My Trung and Truong Quang Cuong and Tran Thi Cam Thi and Hoang Kim Son and Bui Thi Kim Ly. Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu.” European Journal of Biology, vol. 0, no. 0, 2024, pp. -. [Database Container], https://doi.org/10.26650/EurJBiol.2024.1447284


Vancouver

Quan NT, Chi HT, My Trung P, Cuong TQ, Thi TT, Son HK, Ly BT. Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu. European Journal of Biology [Internet]. 8 Nov. 2024 [cited 8 Nov. 2024];0(0):-. Available from: https://doi.org/10.26650/EurJBiol.2024.1447284 doi: 10.26650/EurJBiol.2024.1447284


ISNAD

Quan, NguyenTrung - Chi, HoangThanh - My Trung, Phung - Cuong, TruongQuang - Thi, TranThi Cam - Son, HoangKim - Ly, BuiThi Kim. Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu”. European Journal of Biology 0/0 (Nov. 2024): -. https://doi.org/10.26650/EurJBiol.2024.1447284



ZAMAN ÇİZELGESİ


Gönderim06.03.2024
Kabul27.06.2024
Çevrimiçi Yayınlanma12.09.2024

LİSANS


Attribution-NonCommercial (CC BY-NC)

This license lets others remix, tweak, and build upon your work non-commercially, and although their new works must also acknowledge you and be non-commercial, they don’t have to license their derivative works on the same terms.


PAYLAŞ




İstanbul Üniversitesi Yayınları, uluslararası yayıncılık standartları ve etiğine uygun olarak, yüksek kalitede bilimsel dergi ve kitapların yayınlanmasıyla giderek artan bilimsel bilginin yayılmasına katkıda bulunmayı amaçlamaktadır. İstanbul Üniversitesi Yayınları açık erişimli, ticari olmayan, bilimsel yayıncılığı takip etmektedir.