Journals / European Journal of Biology / 2024 / Volume: 83 Issue: 2

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

Nguyen Quan(Viet Nam National University, Department of Biology- Biotechnology, VNU-HCM)0000-0002-6436-4693
Hoang Thanh Chi(Thu Dau Mot University, Department of Medicine and Pharmacy)0000-0002-6638-1235
Truong Quang Cuong(Bidoup Nui Ba National Park)0000-0001-9159-1018
Tran Thi(Ho Chi Minh City University of Technology– HCMUT, Faculty of Chemical Engineering)0009-0005-6732-2930
Hoang Son(Viet Nam National University, Department of Biology- Biotechnology)0009-0004-0468-8305
Bui Thi Kim Ly(Thu Dau Mot University, Department of Medicine and Pharmacy)0000-0002-8433-7035
Pages
—
Publication Date
2024-12-19
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

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.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Objective: Theaceae is a commodity with high economic value.
📊
Key Findings & Data:Nearly 130 species of Theaceae, many of which are highly endemic, were discovered in Vietnam, including 13 Polyspora species.
💡
Conclusion & Impact: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.
🔬Design:Research Article
📍Scope:2010 Verileri
⚙️Variables:Polyspora huongiana · Phylogeny · matK

Abstract

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.

🔖

Cite This Article

Quan, N., Chi, H. T., Trung, P. M., Cuong, T. Q., Thi, T., Son, H., Ly, B. T. K. (2024). Using Chloroplast Regions accD, matK, rbcL, and ycf-1 for Phylogeny Construction in Polyspora huongiana Orel, Curry & Luu. European Journal of Biology, Volume: 83 Issue: 2. https://doi.org/10.26650/EurJBiol.2024.1447284

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (36)

  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. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. Hebert PD, Cywinska A, Ball SL, deWaard JR. Biolog-ical identifications through DNA barcodes. Proc Biol Sci. 2003;270(1512):313-321. google scholar
  36. 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