PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING

PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING

Quercus is the largest genus of the family Fagaceae in the world and the second-largest in Vietnam, with approximately 50 species. However, the phylogeny study of the Quercus genus in Vietnam has yet to be thoroughly explored. In this study, we utilize the genome-wide single- nucleotide polymorphism...

Mô tả đầy đủ

Đã lưu trong:
Chi tiết về thư mục
Những tác giả chính: Ngoc, Nguyen Van, Hoàng, Thị Bình
Định dạng: Journal article
Ngôn ngữ:English
Được phát hành: ACADEMIA JOURNAL OF BIOLOGY 2024
Những chủ đề:
Flora, MIG-seq, NGS, Phylogeny, Oak
Truy cập trực tuyến:https://scholar.dlu.edu.vn/handle/123456789/3387
Các nhãn: Thêm thẻ
Không có thẻ, Là người đầu tiên thẻ bản ghi này!
Thư viện lưu trữ: Thư viện Trường Đại học Đà Lạt
id oai:scholar.dlu.edu.vn:123456789-3387
record_format dspace
institution Thư viện Trường Đại học Đà Lạt
collection Thư viện số
language English
topic Flora, MIG-seq, NGS, Phylogeny, Oak
spellingShingle Flora, MIG-seq, NGS, Phylogeny, Oak
Ngoc, Nguyen Van
Hoàng, Thị Bình
PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING
description Quercus is the largest genus of the family Fagaceae in the world and the second-largest in Vietnam, with approximately 50 species. However, the phylogeny study of the Quercus genus in Vietnam has yet to be thoroughly explored. In this study, we utilize the genome-wide single- nucleotide polymorphisms (SNPs) data obtained through Multiplexed Inter Simple Sequence Repeat Genotyping by sequencing (MIG-seq) to explore the phylogenetic relationships among Quercus species in Vietnam. The results of this study reveal that all Quercus species in Vietnam belong to subgenus Cerris and the phylogenetic analysis strongly supports the recognition of two infrageneric sections: Quercus and Ilex section for the Vietnamese Quercus. These results also confirm that the monophyly of Quercus in Vietnam is strongly supported by both morphological and molecular data. The results of this study also align entirely with previous research, indicating that Quercus species in Asia fall under the subgenus Cerris, comprising two sections: section Ilex and section Cyclobalanopsis.
format Journal article
author Ngoc, Nguyen Van
Hoàng, Thị Bình
author_facet Ngoc, Nguyen Van
Hoàng, Thị Bình
author_sort Ngoc, Nguyen Van
title PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING
title_short PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING
title_full PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING
title_fullStr PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING
title_full_unstemmed PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING
title_sort phylogenetic relationships of quercus species (fagaceae) in vietnam based on multiplexed inter simple sequence repeat genotyping by sequencing
publisher ACADEMIA JOURNAL OF BIOLOGY
publishDate 2024
url https://scholar.dlu.edu.vn/handle/123456789/3387
_version_ 1798257017492602880
spelling oai:scholar.dlu.edu.vn:123456789-33872024-04-08T08:11:46Z PHYLOGENETIC RELATIONSHIPS OF Quercus SPECIES (FAGACEAE) IN VIETNAM BASED ON MULTIPLEXED INTER SIMPLE SEQUENCE REPEAT GENOTYPING BY SEQUENCING Ngoc, Nguyen Van Hoàng, Thị Bình Flora, MIG-seq, NGS, Phylogeny, Oak Quercus is the largest genus of the family Fagaceae in the world and the second-largest in Vietnam, with approximately 50 species. However, the phylogeny study of the Quercus genus in Vietnam has yet to be thoroughly explored. In this study, we utilize the genome-wide single- nucleotide polymorphisms (SNPs) data obtained through Multiplexed Inter Simple Sequence Repeat Genotyping by sequencing (MIG-seq) to explore the phylogenetic relationships among Quercus species in Vietnam. The results of this study reveal that all Quercus species in Vietnam belong to subgenus Cerris and the phylogenetic analysis strongly supports the recognition of two infrageneric sections: Quercus and Ilex section for the Vietnamese Quercus. These results also confirm that the monophyly of Quercus in Vietnam is strongly supported by both morphological and molecular data. The results of this study also align entirely with previous research, indicating that Quercus species in Asia fall under the subgenus Cerris, comprising two sections: section Ilex and section Cyclobalanopsis. 46 1 99-108 2024-04-08T07:46:00Z 2024-04-08T07:46:00Z 2024-03-21 Journal article Bài báo đăng trên tạp chí trong nước (có ISSN), bao gồm book chapter https://scholar.dlu.edu.vn/handle/123456789/3387 10.15625/2615-9023/19721 en ACADEMIA JOURNAL OF BIOLOGY 2815-5920 Ban N. T., 2005. Vietnam plant checklist, Vol. 2. Agriculture Publishers, Hanoi National University (In Vietnamese). Binh H. T., Ngoc N. V., Bon T. N., Tagane S., Yahara T., 2018a. A new species and two new records of Quercus (Fagaceae) from northern Vietnam. PhytoKeys, 92: 1–15. https://doi.org/10.3897/phytokeys.92.21831 Binh H. T., Ngoc N. V., Tagane S., Toyama H., Mase K., Mitsuyuki C., Strijk J. S., Suyama Y., Yahara T., 2018b. A taxonomic study of Quercus langbianensis complex based on morphology, and DNA barcodes of classicand next-generation sequences. PhytoKeys, 95: 37–70. https://doi.org/ 10.3897/phytokeys.95.21126 Binh H. T., Ngoc N. V., Tai V. A., Son H. T., Tagane S., Yahara T., 2018c. Quercus trungkhanhensis (Fagaceae), a new species from Cao Vit Gibbon Conservation Area, Cao Bang Province, north-eastern Vietnam. Acta Phytotaxonomica et Geobotanica, 69(1): 53–61. https://doi.org/10.18942/apg. 201713 Binh H. T., Ngoc N. V., Son H. T., Tagane S., Yahara T., 2021. Quercus ngochoaensis (Fagaceae), a new species from Ba Vi National Park, northern, Vietnam. Phytotaxa, 516(3): 283–288. https://doi.org/10.11646/phytotaxa.516.3.7 Bolger A. M., Lohse M., Usadel B., 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15): 2114–2120. https://doi.org/ 10.1093/bioinformatics/btu170 Camus A., 1936–1954. Les Chênes. Monographie du genre Quercus et Monographie du genre Lithocarpus. Paul Lechevalier Edition, Paris. Catchen J. M., Hohenlohe P. A., Bassham S., Amores A., Cresko W. A., 2013. Stacks: An analysis tool set for population genomics. Molecular Ecology, 22(11): 3124–3140. https://doi.org/10.1111/mec. 12354 Cavender‐Bares J., González‐Rodríguez A., Eaton D. A., Hipp A. A., Beulke A., Manos P. S., 2015. Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach. Molecular ecology, 24(14): 3668–3687. Darriba D., Taboada G. L., Doallo R., Posada D., 2012. jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9: e772. Denk T., Grimm G. W., 2010. The oaks of western Eurasia: traditional classifications and evidence from two nuclear markers. Taxon, 59: 351–366. Doyle J. J., Doyle J. L., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19: 11–15. Fitz-Gibbon S., Hipp A. L., Pham K. K., Manos P. S., Sork V. L., 2017. Phylogenomic inferences from reference- mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus). Genome, 60(9): 743–755. Hipp A. L., Eaton D. A., Cavender-Bares J., Fitzek E., Nipper R., & Manos P. S., 2014. A framework phylogeny of the American oak clade based on sequenced RAD data. PloS one, 9(4): e93975. Ho P. H., 2000., An illustrated flora of Vietnam (Vol. 2) Young Publishing House, Ho Chi Minh City, pp. 982. Hubert F., Grimm G. W., Jousselin E., Berry V., Franc A., Kremer A., 2014. Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus. Systematics and Biodiversity, 12(4): 405– 423. http://dx.doi.org/10.1080/14772000. 2014.941037 Li Q., Zhang J., Coombes A., 2016. Quercus lineata (Fagaceae): new distribution records from China and Vietnam and its leaf anatomical features. Phytotaxa, 266(3): 226–230. https://doi.org/ 10.11646/phytotaxa.266.3.7 Manos P. S., Stanford, A. M., 2001. The historical biogeography of Fagaceae: tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere. International Journal of Plant Sciences, 162(S6): S77–S93. McVay J. D., Hipp A. L., Manos P. S., 2017. A genetic legacy of introgression confounds phylogeny and biogeography in oaks. Proceedings of the Royal Society B: Biological Sciences, 284(1854): 20170300. Menitsky Y. L., 2005. Oaks of Asia. Science Publishers, Enfield, NH, USA. Ngoc N. V., Binh H. T., Nagahama A., Tagane S., Toyama H., Matsuo A., Suyama Y., Yahara T., 2021. Morphological and molecular evidence reveals three new species of Lithocarpus (Fagaceae) from Bidoup-Nui Ba National Park, Vietnam. PhytoKeys, 186: 73–92. https://doi.org/10.3897/phytokeys.186.698 78 Ngoc N. V., Binh H. T., Son H. T., Suyama Y., Yahara T., 2022a. A new species of Quercus genus (Fagaceae) from Son Tra Peninsula, Central Vietnam. PhytoKeys, 206: 61–73. https://doi.org/10.3897/ phytokeys.206.85635 Ngoc N. V., Binh H. T., 2022b. Quercus mangdenensis, a new species of Quercus (Fagaceae) from Kon Tum Province, Vietnam. PhytoKeys, 215: 73–79. https://doi.org/10.3897/phytokeys.215.936 84 Nixon K. C., 1993. Infrageneric classification of Quercus (Fagaceae) and typification of sectional names. Annales des Sciences Forestieres, 50(Supplement): 25–34. https://doi.org/10.1051/forest:19930701 Nixon K. C., 2006. Global and neotropical distribution and diversity of oak (genus Quercus) and oak forests. In: M. Kappelle (Ed.), Ecological Studies (Vol. 185): Ecology and conservation of neotropical montane oak forests. Berlin, Heidelberg: Springer Berlin Heidelberg: 3–13. Oh S. H., Manos P. S., 2008. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences. Taxon, 57: 434–451. Rochette N. C., Rivera-Colon A. G., Catchen J. M., 2019. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology, 28: 4737–4754. Schwarz O., 1936. Entwurf zu einem natürlichen System der Cupuliferen und Phylogenetic relationships of Quercus species der Gattung Quercus L. Notizblatt des Botanischen Gartens und Museums zu Berlin-Dahlem: 1–22. Simeone M. C., Grimm G. W., Papini A., Vessella F., Cardoni S., Tordoni E., Piredda R., Franc A., Denk T., 2016. Plastome data reveal multiple geographic origins of Quercus Group Ilex. PeerJ, 4: e1897. Stamatakis A., 2014. RAxML Version 8: A tool for phylogenetic analysis and post- analysis of large phylogenies. Bioinformatics, 30: 1312–1313. Suyama Y., Matsuki Y., 2015. MIG-seq: An effective PCR-based method for genome- wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Scientific Reports, 5(1): e16968. https://doi.org/10.1038/srep16963 Toyama H., Kajisa T., Tagane S., Mase K., Chhang P., Samreth V., Ma V., Sokh H., Ichihasi R., Onoda Y., Mizoue N., Yahara T., 2015. Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom, Cambodia. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1662): 1–13. https://doi.org/10.1098/rstb.2014.00 08 Valencia-A. S., Rosales J. L. S., Arellano O. J. S., 2016. A new species of Quercus, section Lobatae (Fagaceae) from the Sierra Madre Oriental, Mexico. Phytotaxa, 269(2): 120–126. https://doi.org/ 10.11646/phytotaxa.269.2.5 Yang Y., Zhou T., Qian Z., Zhao G., 2021. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics, 113(3): 1438–1447. ACADEMIA JOURNAL OF BIOLOGY Ha Noi

Những quyển sách tương tự